diff options
Diffstat (limited to 'silx/io')
38 files changed, 12057 insertions, 8002 deletions
diff --git a/silx/io/__init__.py b/silx/io/__init__.py index 4e3cace..96f6708 100644 --- a/silx/io/__init__.py +++ b/silx/io/__init__.py @@ -1,7 +1,7 @@ # coding: utf-8 # /*########################################################################## # -# Copyright (c) 2016 European Synchrotron Radiation Facility +# Copyright (c) 2016-2017 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -26,20 +26,16 @@ __authors__ = ["P. Knobel"] __license__ = "MIT" -__date__ = "20/01/2017" +__date__ = "15/05/2017" -import logging - - -# Init logging once for the whole module -logging.basicConfig() - from .utils import open # pylint:disable=redefined-builtin from .utils import save1D from .utils import is_dataset from .utils import is_file from .utils import is_group +from .utils import is_softlink -__all__ = ["save1D", "is_dataset", "is_file", "is_group"] # avoid to import open with "import *" +# avoid to import open with "import *" +__all__ = ["save1D", "is_dataset", "is_file", "is_group", "is_softlink"] diff --git a/silx/io/commonh5.py b/silx/io/commonh5.py new file mode 100644 index 0000000..0f5ac02 --- /dev/null +++ b/silx/io/commonh5.py @@ -0,0 +1,991 @@ +# coding: utf-8 +# /*########################################################################## +# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +# THE SOFTWARE. +# +# ############################################################################*/ +""" +This module contains generic objects, emulating *h5py* groups, datasets and +files. They are used in :mod:`spech5` and :mod:`fabioh5`. + +.. note:: This module has a dependency on the `h5py <http://www.h5py.org/>`_ + library, which is not a mandatory dependency for `silx`. +""" +import collections +import h5py +import numpy +from silx.third_party import six + +from .utils import is_dataset + +__authors__ = ["V. Valls", "P. Knobel"] +__license__ = "MIT" +__date__ = "21/09/2017" + + +class _MappingProxyType(collections.MutableMapping): + """Read-only dictionary + + This class is available since Python 3.3, but not on earlyer Python + versions. + """ + + def __init__(self, data): + self._data = data + + def __getitem__(self, key): + return self._data[key] + + def __len__(self): + return len(self._data) + + def __iter__(self): + return iter(self._data) + + def get(self, key, default=None): + return self._data.get(key, default) + + def __setitem__(self, key, value): + raise RuntimeError("Cannot modify read-only dictionary") + + def __delitem__(self, key): + raise RuntimeError("Cannot modify read-only dictionary") + + def pop(self, key): + raise RuntimeError("Cannot modify read-only dictionary") + + def clear(self): + raise RuntimeError("Cannot modify read-only dictionary") + + def update(self, key, value): + raise RuntimeError("Cannot modify read-only dictionary") + + def setdefault(self, key): + raise RuntimeError("Cannot modify read-only dictionary") + + +class Node(object): + """This is the base class for all :mod:`spech5` and :mod:`fabioh5` + classes. It represents a tree node, and knows its parent node + (:attr:`parent`). + The API mimics a *h5py* node, with following attributes: :attr:`file`, + :attr:`attrs`, :attr:`name`, and :attr:`basename`. + """ + + def __init__(self, name, parent=None, attrs=None): + self.__parent = parent + self.__basename = name + self.__attrs = {} + if attrs is not None: + self.__attrs.update(attrs) + + def _set_basename(self, name): + self.__basename = name + + @property + def h5py_class(self): + """Returns the h5py classes which is mimicked by this class. It can be + one of `h5py.File, h5py.Group` or `h5py.Dataset` + + :rtype: Class + """ + raise NotImplementedError() + + @property + def parent(self): + """Returns the parent of the node. + + :rtype: Node + """ + return self.__parent + + @property + def file(self): + """Returns the file node of this node. + + :rtype: Node + """ + node = self + while node.__parent is not None: + node = node.__parent + if isinstance(node, File): + return node + else: + return None + + def _set_parent(self, parent): + """Set the parent of this node. + + It do not update the parent object. + + :param Node parent: New parent for this node + """ + self.__parent = parent + + @property + def attrs(self): + """Returns HDF5 attributes of this node. + + :rtype: dict + """ + if self._is_editable(): + return self.__attrs + else: + return _MappingProxyType(self.__attrs) + + @property + def name(self): + """Returns the HDF5 name of this node. + """ + if self.__parent is None: + return "/" + if self.__parent.name == "/": + return "/" + self.basename + return self.__parent.name + "/" + self.basename + + @property + def basename(self): + """Returns the HDF5 basename of this node. + """ + return self.__basename + + def _is_editable(self): + """Returns true if the file is editable or if the node is not linked + to a tree. + + :rtype: bool + """ + f = self.file + return f is None or f.mode == "w" + + +class Dataset(Node): + """This class handles a numpy data object, as a mimicry of a + *h5py.Dataset*. + """ + + def __init__(self, name, data, parent=None, attrs=None): + Node.__init__(self, name, parent, attrs=attrs) + if data is not None: + self._check_data(data) + self.__data = data + + def _check_data(self, data): + """Check that the data provided by the dataset is valid. + + :param numpy.ndarray data: Data associated to the dataset + + :raises TypeError: In the case the data is not valid. + """ + chartype = data.dtype.char + if chartype in ["U", "O"]: + msg = "Type of the dataset '%s' is not supported. Found '%s'." + raise TypeError(msg % (self.name, data.dtype)) + + def _set_data(self, data): + """Set the data exposed by the dataset. + + It have to be called only one time before the data is used. It should + not be edited after use. + + :param numpy.ndarray data: Data associated to the dataset + """ + self._check_data(data) + self.__data = data + + def _get_data(self): + """Returns the exposed data + + :rtype: numpy.ndarray + """ + return self.__data + + @property + def h5py_class(self): + """Returns the h5py classes which is mimicked by this class. It can be + one of `h5py.File, h5py.Group` or `h5py.Dataset` + + :rtype: Class + """ + return h5py.Dataset + + @property + def dtype(self): + """Returns the numpy datatype exposed by this dataset. + + :rtype: numpy.dtype + """ + return self._get_data().dtype + + @property + def shape(self): + """Returns the shape of the data exposed by this dataset. + + :rtype: tuple + """ + if isinstance(self._get_data(), numpy.ndarray): + return self._get_data().shape + else: + return tuple() + + @property + def size(self): + """Returns the size of the data exposed by this dataset. + + :rtype: int + """ + if isinstance(self._get_data(), numpy.ndarray): + return self._get_data().size + else: + # It is returned as float64 1.0 by h5py + return numpy.float64(1.0) + + def __len__(self): + """Returns the size of the data exposed by this dataset. + + :rtype: int + """ + if isinstance(self._get_data(), numpy.ndarray): + return len(self._get_data()) + else: + # It is returned as float64 1.0 by h5py + raise TypeError("Attempt to take len() of scalar dataset") + + def __getitem__(self, item): + """Returns the slice of the data exposed by this dataset. + + :rtype: numpy.ndarray + """ + if not isinstance(self._get_data(), numpy.ndarray): + if item == Ellipsis: + return numpy.array(self._get_data()) + elif item == tuple(): + return self._get_data() + else: + raise ValueError("Scalar can only be reached with an ellipsis or an empty tuple") + return self._get_data().__getitem__(item) + + def __str__(self): + basename = self.name.split("/")[-1] + return '<HDF5-like dataset "%s": shape %s, type "%s">' % \ + (basename, self.shape, self.dtype.str) + + def __getslice__(self, i, j): + """Returns the slice of the data exposed by this dataset. + + Deprecated but still in use for python 2.7 + + :rtype: numpy.ndarray + """ + return self.__getitem__(slice(i, j, None)) + + @property + def value(self): + """Returns the data exposed by this dataset. + + Deprecated by h5py. It is prefered to use indexing `[()]`. + + :rtype: numpy.ndarray + """ + return self._get_data() + + @property + def compression(self): + """Returns compression as provided by `h5py.Dataset`. + + There is no compression.""" + return None + + @property + def compression_opts(self): + """Returns compression options as provided by `h5py.Dataset`. + + There is no compression.""" + return None + + @property + def chunks(self): + """Returns chunks as provided by `h5py.Dataset`. + + There is no chunks.""" + return None + + def __array__(self, dtype=None): + # Special case for (0,)*-shape datasets + if numpy.product(self.shape) == 0: + return self[()] + else: + return numpy.array(self[...], dtype=self.dtype if dtype is None else dtype) + + def __iter__(self): + """Iterate over the first axis. TypeError if scalar.""" + if len(self.shape) == 0: + raise TypeError("Can't iterate over a scalar dataset") + return self._get_data().__iter__() + + # make comparisons and operations on the data + def __eq__(self, other): + """When comparing datasets, compare the actual data.""" + if is_dataset(other): + return self[()] == other[()] + return self[()] == other + + def __add__(self, other): + return self[()] + other + + def __radd__(self, other): + return other + self[()] + + def __sub__(self, other): + return self[()] - other + + def __rsub__(self, other): + return other - self[()] + + def __mul__(self, other): + return self[()] * other + + def __rmul__(self, other): + return other * self[()] + + def __truediv__(self, other): + return self[()] / other + + def __rtruediv__(self, other): + return other / self[()] + + def __floordiv__(self, other): + return self[()] // other + + def __rfloordiv__(self, other): + return other // self[()] + + def __neg__(self): + return -self[()] + + def __abs__(self): + return abs(self[()]) + + def __float__(self): + return float(self[()]) + + def __int__(self): + return int(self[()]) + + def __bool__(self): + if self[()]: + return True + return False + + def __nonzero__(self): + # python 2 + return self.__bool__() + + def __ne__(self, other): + if is_dataset(other): + return self[()] != other[()] + else: + return self[()] != other + + def __lt__(self, other): + if is_dataset(other): + return self[()] < other[()] + else: + return self[()] < other + + def __le__(self, other): + if is_dataset(other): + return self[()] <= other[()] + else: + return self[()] <= other + + def __gt__(self, other): + if is_dataset(other): + return self[()] > other[()] + else: + return self[()] > other + + def __ge__(self, other): + if is_dataset(other): + return self[()] >= other[()] + else: + return self[()] >= other + + def __getattr__(self, item): + """Proxy to underlying numpy array methods. + """ + data = self._get_data() + if hasattr(data, item): + return getattr(data, item) + + raise AttributeError("Dataset has no attribute %s" % item) + + +class _LinkToDataset(Dataset): + """Virtual dataset providing link to another dataset""" + + def __init__(self, name, target, parent=None): + Dataset.__init__(self, name, data=None, parent=parent) + self.__target = target + + def _get_data(self): + return self.__target._get_data() + + @property + def attrs(self): + return self.__target.attrs + + +class LazyLoadableDataset(Dataset): + """Abstract dataset which provides a lazy loading of the data. + + The class has to be inherited and the :meth:`_create_data` method has to be + implemented to return the numpy data exposed by the dataset. This factory + method is only called once, when the data is needed. + """ + + def __init__(self, name, parent=None, attrs=None): + super(LazyLoadableDataset, self).__init__(name, None, parent, attrs=attrs) + self._is_initialized = False + + def _create_data(self): + """ + Factory to create the data exposed by the dataset when it is needed. + + It has to be implemented for the class to work. + + :rtype: numpy.ndarray + """ + raise NotImplementedError() + + def _get_data(self): + """Returns the data exposed by the dataset. + + Overwrite Dataset method :meth:`_get_data` to implement the lazy + loading feature. + + :rtype: numpy.ndarray + """ + if not self._is_initialized: + data = self._create_data() + # is_initialized before set_data to avoid infinit initialization + # is case of wrong check of the data + self._is_initialized = True + self._set_data(data) + return super(LazyLoadableDataset, self)._get_data() + + +class SoftLink(Node): + """This class is a tree node that mimics a *h5py.Softlink*. + + In this implementation, the path to the target must be absolute. + """ + def __init__(self, name, path, parent=None): + assert str(path).startswith("/") # TODO: h5py also allows a relative path + + Node.__init__(self, name, parent) + + # attr target defined for spech5 backward compatibility + self.target = str(path) + + @property + def h5py_class(self): + """Returns the h5py class which is mimicked by this class + (:class:`h5py.SoftLink`). + + :rtype: Class + """ + return h5py.SoftLink + + @property + def path(self): + """Soft link value. Not guaranteed to be a valid path.""" + return self.target + + +class Group(Node): + """This class mimics a `h5py.Group`.""" + + def __init__(self, name, parent=None, attrs=None): + Node.__init__(self, name, parent, attrs=attrs) + self.__items = collections.OrderedDict() + + def _get_items(self): + """Returns the child items as a name-node dictionary. + + :rtype: dict + """ + return self.__items + + def add_node(self, node): + """Add a child to this group. + + :param Node node: Child to add to this group + """ + self._get_items()[node.basename] = node + node._set_parent(self) + + @property + def h5py_class(self): + """Returns the h5py classes which is mimicked by this class. + + It returns `h5py.Group` + + :rtype: Class + """ + return h5py.Group + + def _get(self, name, getlink): + """If getlink is True and name points to an existing SoftLink, this + SoftLink is returned. In all other situations, we try to return a + Group or Dataset, or we raise a KeyError if we fail.""" + if "/" not in name: + result = self._get_items()[name] + elif name.startswith("/"): + root = self.file + if name == "/": + return root + result = root._get(name[1:], getlink) + else: + path = name.split("/") + result = self + for item_name in path: + if isinstance(result, SoftLink): + # traverse links + l_name, l_target = result.name, result.path + result = result.file.get(l_target) + if result is None: + raise KeyError( + "Unable to open object (broken SoftLink %s -> %s)" % + (l_name, l_target)) + if not item_name: + # trailing "/" in name (legal for accessing Groups only) + if isinstance(result, Group): + continue + if not isinstance(result, Group): + raise KeyError("Unable to open object (Component not found)") + result = result._get_items()[item_name] + + if isinstance(result, SoftLink) and not getlink: + link = result + target = result.file.get(link.path) + if result is None: + msg = "Unable to open object (broken SoftLink %s -> %s)" + raise KeyError(msg % (link.name, link.path)) + # Convert SoftLink into typed group/dataset + if isinstance(target, Group): + result = _LinkToGroup(name=link.basename, target=target, parent=link.parent) + elif isinstance(target, Dataset): + result = _LinkToDataset(name=link.basename, target=target, parent=link.parent) + else: + raise TypeError("Unexpected target type %s" % type(target)) + + return result + + def get(self, name, default=None, getclass=False, getlink=False): + """Retrieve an item or other information. + + If getlink only is true, the returned value is always `h5py.HardLink`, + because this implementation do not use links. Like the original + implementation. + + :param str name: name of the item + :param object default: default value returned if the name is not found + :param bool getclass: if true, the returned object is the class of the object found + :param bool getlink: if true, links object are returned instead of the target + :return: An object, else None + :rtype: object + """ + if name not in self: + return default + + node = self._get(name, getlink=True) + if isinstance(node, SoftLink) and not getlink: + # get target + try: + node = self._get(name, getlink=False) + except KeyError: + return default + elif not isinstance(node, SoftLink) and getlink: + # ExternalLink objects don't exist in silx, so it must be a HardLink + node = h5py.HardLink() + + if getclass: + if hasattr(node, "h5py_class"): + obj = node.h5py_class + else: + obj = node.__class__ + else: + obj = node + return obj + + def __setitem__(self, name, obj): + """Add an object to the group. + + :param str name: Location on the group to store the object. + This path name must not exists. + :param object obj: Object to store on the file. According to the type, + the behaviour will not be the same. + + - `commonh5.SoftLink`: Create the corresponding link. + - `numpy.ndarray`: The array is converted to a dataset object. + - `commonh5.Node`: A hard link should be created pointing to the + given object. This implementation uses a soft link. + If the node do not have parent it is connected to the tree + without using a link (that's a hard link behaviour). + - other object: Convert first the object with ndarray and then + store it. ValueError if the resulting array dtype is not + supported. + """ + if name in self: + # From the h5py API + raise RuntimeError("Unable to create link (name already exists)") + + elements = name.rsplit("/", 1) + if len(elements) == 1: + parent = self + basename = elements[0] + else: + group_path, basename = elements + if group_path in self: + parent = self[group_path] + else: + parent = self.create_group(group_path) + + if isinstance(obj, SoftLink): + obj._set_basename(basename) + node = obj + elif isinstance(obj, Node): + if obj.parent is None: + obj._set_basename(basename) + node = obj + else: + node = SoftLink(basename, obj.name) + elif isinstance(obj, numpy.dtype): + node = Dataset(basename, data=obj) + elif isinstance(obj, numpy.ndarray): + node = Dataset(basename, data=obj) + else: + data = numpy.array(obj) + try: + node = Dataset(basename, data=data) + except TypeError as e: + raise ValueError(e.args[0]) + + parent.add_node(node) + + def __getitem__(self, name): + """Return a child from his name. + + :param name str: name of a member or a path throug members using '/' + separator. A '/' as a prefix access to the root item of the tree. + :rtype: Node + """ + if name is None or name == "": + raise ValueError("No name") + return self._get(name, getlink=False) + + def __contains__(self, name): + """Returns true if name is an existing child of this group. + + :rtype: bool + """ + if "/" not in name: + return name in self._get_items() + + if name.startswith("/"): + # h5py allows to access any valid full path from any group + node = self.file + else: + node = self + + name = name.lstrip("/") + basenames = name.split("/") + for basename in basenames: + if basename.strip() == "": + # presence of a trailing "/" in name + # (OK for groups, not for datasets) + if isinstance(node, SoftLink): + # traverse links + node = node.file.get(node.path, getlink=False) + if node is None: + # broken link + return False + if node.h5py_class == h5py.Dataset: + return False + continue + if basename not in node._get_items(): + return False + node = node[basename] + + return True + + def __len__(self): + """Returns the number of children contained in this group. + + :rtype: int + """ + return len(self._get_items()) + + def __iter__(self): + """Iterate over member names""" + for x in self._get_items().__iter__(): + yield x + + if six.PY2: + def keys(self): + """Returns a list of the children's names.""" + return self._get_items().keys() + + def values(self): + """Returns a list of the children nodes (groups and datasets). + + .. versionadded:: 0.6 + """ + return self._get_items().values() + + def items(self): + """Returns a list of tuples containing (name, node) pairs. + """ + return self._get_items().items() + + else: + def keys(self): + """Returns an iterator over the children's names in a group.""" + return self._get_items().keys() + + def values(self): + """Returns an iterator over the children nodes (groups and datasets) + in a group. + + .. versionadded:: 0.6 + """ + return self._get_items().values() + + def items(self): + """Returns items iterator containing name-node mapping. + + :rtype: iterator + """ + return self._get_items().items() + + def visit(self, func, visit_links=False): + """Recursively visit all names in this group and subgroups. + See the documentation for `h5py.Group.visit` for more help. + + :param func: Callable (function, method or callable object) + :type func: function + """ + origin_name = self.name + return self._visit(func, origin_name, visit_links) + + def visititems(self, func, visit_links=False): + """Recursively visit names and objects in this group. + See the documentation for `h5py.Group.visititems` for more help. + + :param func: Callable (function, method or callable object) + :type func: function + :param bool visit_links: If *False*, ignore links. If *True*, + call `func(name)` for links and recurse into target groups. + """ + origin_name = self.name + return self._visit(func, origin_name, visit_links, + visititems=True) + + def _visit(self, func, origin_name, + visit_links=False, visititems=False): + """ + + :param origin_name: name of first group that initiated the recursion + This is used to compute the relative path from each item's + absolute path. + """ + for member in self.values(): + ret = None + if not isinstance(member, SoftLink) or visit_links: + relative_name = member.name[len(origin_name):] + # remove leading slash and unnecessary trailing slash + relative_name = relative_name.strip("/") + if visititems: + ret = func(relative_name, member) + else: + ret = func(relative_name) + if ret is not None: + return ret + if isinstance(member, Group): + member._visit(func, origin_name, visit_links, visititems) + + def create_group(self, name): + """Create and return a new subgroup. + + Name may be absolute or relative. Fails if the target name already + exists. + + :param str name: Name of the new group + """ + if not self._is_editable(): + raise RuntimeError("File is not editable") + if name in self: + raise ValueError("Unable to create group (name already exists)") + + if name.startswith("/"): + name = name[1:] + return self.file.create_group(name) + + elements = name.split('/') + group = self + for basename in elements: + if basename in group: + group = group[basename] + if not isinstance(group, Group): + raise RuntimeError("Unable to create group (group parent is missing") + else: + node = Group(basename) + group.add_node(node) + group = node + return group + + def create_dataset(self, name, shape=None, dtype=None, data=None, **kwds): + """Create and return a sub dataset. + + :param str name: Name of the dataset. + :param shape: Dataset shape. Use "()" for scalar datasets. + Required if "data" isn't provided. + :param dtype: Numpy dtype or string. + If omitted, dtype('f') will be used. + Required if "data" isn't provided; otherwise, overrides data + array's dtype. + :param numpy.ndarray data: Provide data to initialize the dataset. + If used, you can omit shape and dtype arguments. + :param kwds: Extra arguments. Nothing yet supported. + """ + if not self._is_editable(): + raise RuntimeError("File is not editable") + if len(kwds) > 0: + raise TypeError("Extra args provided, but nothing supported") + if "/" in name: + raise TypeError("Path are not supported") + if data is None: + if dtype is None: + dtype = numpy.float + data = numpy.empty(shape=shape, dtype=dtype) + elif dtype is not None: + data = data.astype(dtype) + dataset = Dataset(name, data) + self.add_node(dataset) + return dataset + + +class _LinkToGroup(Group): + """Virtual group providing link to another group""" + + def __init__(self, name, target, parent=None): + Group.__init__(self, name, parent=parent) + self.__target = target + + def _get_items(self): + return self.__target._get_items() + + @property + def attrs(self): + return self.__target.attrs + + +class LazyLoadableGroup(Group): + """Abstract group which provides a lazy loading of the child. + + The class has to be inherited and the :meth:`_create_child` method has + to be implemented to add (:meth:`_add_node`) all children. This factory + is only called once, when children are needed. + """ + + def __init__(self, name, parent=None, attrs=None): + Group.__init__(self, name, parent, attrs) + self.__is_initialized = False + + def _get_items(self): + """Returns the internal structure which contains the children. + + It overwrite method :meth:`_get_items` to implement the lazy + loading feature. + + :rtype: dict + """ + if not self.__is_initialized: + self.__is_initialized = True + self._create_child() + return Group._get_items(self) + + def _create_child(self): + """ + Factory to create the child contained by the group when it is needed. + + It has to be implemented to work. + """ + raise NotImplementedError() + + +class File(Group): + """This class is the special :class:`Group` that is the root node + of the tree structure. It mimics `h5py.File`.""" + + def __init__(self, name=None, mode=None, attrs=None): + """ + Constructor + + :param str name: File name if it exists + :param str mode: Access mode + - "r": Read-only. Methods :meth:`create_dataset` and + :meth:`create_group` are locked. + - "w": File is editable. Methods :meth:`create_dataset` and + :meth:`create_group` are available. + :param dict attrs: Default attributes + """ + Group.__init__(self, name="", parent=None, attrs=attrs) + self._file_name = name + if mode is None: + mode = "r" + assert(mode in ["r", "w"]) + self._mode = mode + + @property + def filename(self): + return self._file_name + + @property + def mode(self): + return self._mode + + @property + def h5py_class(self): + """Returns the :class:`h5py.File` class""" + return h5py.File + + def __enter__(self): + return self + + def __exit__(self, exc_type, exc_val, exc_tb): + self.close() + + def close(self): + """Close the object, and free up associated resources. + """ + # should be implemented in subclass + pass diff --git a/silx/io/convert.py b/silx/io/convert.py new file mode 100644 index 0000000..41f1e36 --- /dev/null +++ b/silx/io/convert.py @@ -0,0 +1,302 @@ +# coding: utf-8 +# /*########################################################################## +# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +# THE SOFTWARE. +# +# ############################################################################*/ +"""This module provides classes and function to convert file formats supported +by *silx* into HDF5 file. Currently, SPEC file and fabio images are the +supported formats. + +Read the documentation of :mod:`silx.io.spech5` and :mod:`silx.io.fabioh5` for +information on the structure of the output HDF5 files. + +Strings are written to the HDF5 datasets as fixed-length ASCII (NumPy *S* type). +This is done in order to produce files that have maximum compatibility with +other HDF5 libraries, as recommended in the +`h5py documentation <http://docs.h5py.org/en/latest/strings.html#how-to-store-text-strings>`_. + +If you read the files back with *h5py* in Python 3, you will recover strings +as bytes, which you should decode to transform them into python strings:: + + >>> import h5py + >>> f = h5py.File("myfile.h5") + >>> f["/1.1/instrument/specfile/scan_header"][0] + b'#S 94 ascan del -0.5 0.5 20 1' + >>> f["/1.1/instrument/specfile/scan_header"][0].decode() + '#S 94 ascan del -0.5 0.5 20 1' + +Arrays of strings, such as file and scan headers, are stored as fixed-length +strings. The length of all strings in an array is equal to the length of the +longest string. Shorter strings are right-padded with blank spaces. + +.. note:: This module has a dependency on the `h5py <http://www.h5py.org/>`_ + library, which is not a mandatory dependency for `silx`. You might need + to install it if you don't already have it. +""" + +import numpy +import logging + +import silx.io +from silx.io import is_dataset, is_group, is_softlink + +__authors__ = ["P. Knobel"] +__license__ = "MIT" +__date__ = "14/09/2017" + +_logger = logging.getLogger(__name__) + +try: + import h5py +except ImportError as e: + _logger.error("Module " + __name__ + " requires h5py") + raise e + + +def _create_link(h5f, link_name, target_name, + link_type="soft", overwrite_data=False): + """Create a link in a HDF5 file + + If member with name ``link_name`` already exists, delete it first or + ignore link depending on global param ``overwrite_data``. + + :param h5f: :class:`h5py.File` object + :param link_name: Link path + :param target_name: Handle for target group or dataset + :param str link_type: "soft" or "hard" + :param bool overwrite_data: If True, delete existing member (group, + dataset or link) with the same name. Default is False. + """ + if link_name not in h5f: + _logger.debug("Creating link " + link_name + " -> " + target_name) + elif overwrite_data: + _logger.warn("Overwriting " + link_name + " with link to " + + target_name) + del h5f[link_name] + else: + _logger.warn(link_name + " already exist. Can't create link to " + + target_name) + return None + + if link_type == "hard": + h5f[link_name] = h5f[target_name] + elif link_type == "soft": + h5f[link_name] = h5py.SoftLink(target_name) + else: + raise ValueError("link_type must be 'hard' or 'soft'") + + +class Hdf5Writer(object): + """Converter class to write the content of a data file to a HDF5 file. + """ + def __init__(self, + h5path='/', + overwrite_data=False, + link_type="soft", + create_dataset_args=None, + min_size=500): + """ + + :param h5path: Target path where the scan groups will be written + in the output HDF5 file. + :param bool overwrite_data: + See documentation of :func:`write_to_h5` + :param str link_type: ``"hard"`` or ``"soft"`` (default) + :param dict create_dataset_args: Dictionary of args you want to pass to + ``h5py.File.create_dataset``. + See documentation of :func:`write_to_h5` + :param int min_size: + See documentation of :func:`write_to_h5` + """ + self.h5path = h5path + if not h5path.startswith("/"): + # target path must be absolute + self.h5path = "/" + h5path + if not self.h5path.endswith("/"): + self.h5path += "/" + + self._h5f = None + """h5py.File object, assigned in :meth:`write`""" + + if create_dataset_args is None: + create_dataset_args = {} + self.create_dataset_args = create_dataset_args + + self.min_size = min_size + + self.overwrite_data = overwrite_data # boolean + + self.link_type = link_type + """'soft' or 'hard' """ + + self._links = [] + """List of *(link_path, target_path)* tuples.""" + + def write(self, infile, h5f): + """Do the conversion from :attr:`sfh5` (Spec file) to *h5f* (HDF5) + + All the parameters needed for the conversion have been initialized + in the constructor. + + :param infile: :class:`SpecH5` object + :param h5f: :class:`h5py.File` instance + """ + # Recurse through all groups and datasets to add them to the HDF5 + self._h5f = h5f + infile.visititems(self.append_member_to_h5, visit_links=True) + + # Handle the attributes of the root group + root_grp = h5f[self.h5path] + for key in infile.attrs: + if self.overwrite_data or key not in root_grp.attrs: + root_grp.attrs.create(key, + numpy.string_(infile.attrs[key])) + + # Handle links at the end, when their targets are created + for link_name, target_name in self._links: + _create_link(self._h5f, link_name, target_name, + link_type=self.link_type, + overwrite_data=self.overwrite_data) + self._links = [] + + def append_member_to_h5(self, h5like_name, obj): + """Add one group or one dataset to :attr:`h5f`""" + h5_name = self.h5path + h5like_name.lstrip("/") + + if is_softlink(obj): + # links to be created after all groups and datasets + h5_target = self.h5path + obj.path.lstrip("/") + self._links.append((h5_name, h5_target)) + + elif is_dataset(obj): + _logger.debug("Saving dataset: " + h5_name) + + member_initially_exists = h5_name in self._h5f + + if self.overwrite_data and member_initially_exists: + _logger.warn("Overwriting dataset: " + h5_name) + del self._h5f[h5_name] + + if self.overwrite_data or not member_initially_exists: + # fancy arguments don't apply to small dataset + if obj.size < self.min_size: + ds = self._h5f.create_dataset(h5_name, data=obj.value) + else: + ds = self._h5f.create_dataset(h5_name, data=obj.value, + **self.create_dataset_args) + else: + ds = self._h5f[h5_name] + + # add HDF5 attributes + for key in obj.attrs: + if self.overwrite_data or key not in ds.attrs: + ds.attrs.create(key, numpy.string_(obj.attrs[key])) + + if not self.overwrite_data and member_initially_exists: + _logger.warn("Ignoring existing dataset: " + h5_name) + + elif is_group(obj): + if h5_name not in self._h5f: + _logger.debug("Creating group: " + h5_name) + grp = self._h5f.create_group(h5_name) + else: + grp = self._h5f[h5_name] + + # add HDF5 attributes + for key in obj.attrs: + if self.overwrite_data or key not in grp.attrs: + grp.attrs.create(key, numpy.string_(obj.attrs[key])) + + +def write_to_h5(infile, h5file, h5path='/', mode="a", + overwrite_data=False, link_type="soft", + create_dataset_args=None, min_size=500): + """Write content of a h5py-like object into a HDF5 file. + + :param infile: Path of input file, or :class:`commonh5.File` object + or :class:`commonh5.Group` object + :param h5file: Path of output HDF5 file or HDF5 file handle + (`h5py.File` object) + :param str h5path: Target path in HDF5 file in which scan groups are created. + Default is root (``"/"``) + :param str mode: Can be ``"r+"`` (read/write, file must exist), + ``"w"`` (write, existing file is lost), ``"w-"`` (write, fail + if exists) or ``"a"`` (read/write if exists, create otherwise). + This parameter is ignored if ``h5file`` is a file handle. + :param bool overwrite_data: If ``True``, existing groups and datasets can be + overwritten, if ``False`` they are skipped. This parameter is only + relevant if ``file_mode`` is ``"r+"`` or ``"a"``. + :param str link_type: *"soft"* (default) or *"hard"* + :param dict create_dataset_args: Dictionary of args you want to pass to + ``h5py.File.create_dataset``. This allows you to specify filters and + compression parameters. Don't specify ``name`` and ``data``. + These arguments are only applied to datasets larger than 1MB. + :param int min_size: Minimum number of elements in a dataset to apply + chunking and compression. Default is 500. + + The structure of the spec data in an HDF5 file is described in the + documentation of :mod:`silx.io.spech5`. + """ + writer = Hdf5Writer(h5path=h5path, + overwrite_data=overwrite_data, + link_type=link_type, + create_dataset_args=create_dataset_args, + min_size=min_size) + + # both infile and h5file can be either file handle or a file name: 4 cases + if not isinstance(h5file, h5py.File) and not is_group(infile): + with silx.io.open(infile) as h5pylike: + with h5py.File(h5file, mode) as h5f: + writer.write(h5pylike, h5f) + elif isinstance(h5file, h5py.File) and not is_group(infile): + with silx.io.open(infile) as h5pylike: + writer.write(h5pylike, h5file) + elif is_group(infile) and not isinstance(h5file, h5py.File): + with h5py.File(h5file, mode) as h5f: + writer.write(infile, h5f) + else: + writer.write(infile, h5file) + + +def convert(infile, h5file, mode="w-", create_dataset_args=None): + """Convert a supported file into an HDF5 file, write scans into the + root group (``/``). + + This is a convenience shortcut to call:: + + write_to_h5(h5like, h5file, h5path='/', + mode="w-", link_type="soft") + + :param infile: Path of input file or :class:`commonh5.File` object + or :class:`commonh5.Group` object + :param h5file: Path of output HDF5 file, or h5py.File object + :param mode: Can be ``"w"`` (write, existing file is + lost), ``"w-"`` (write, fail if exists). This is ignored + if ``h5file`` is a file handle. + :param create_dataset_args: Dictionary of args you want to pass to + ``h5py.File.create_dataset``. This allows you to specify filters and + compression parameters. Don't specify ``name`` and ``data``. + """ + if mode not in ["w", "w-"]: + raise IOError("File mode must be 'w' or 'w-'. Use write_to_h5" + + " to append data to an existing HDF5 file.") + write_to_h5(infile, h5file, h5path='/', mode=mode, + create_dataset_args=create_dataset_args) diff --git a/silx/io/dictdump.py b/silx/io/dictdump.py index ae7a457..1860b7f 100644 --- a/silx/io/dictdump.py +++ b/silx/io/dictdump.py @@ -41,13 +41,13 @@ else: h5py_missing = False from .configdict import ConfigDict -from .utils import is_group, is_file - -from silx.io import open as h5open +from .utils import is_group +from .utils import is_file as is_h5_file_like +from .utils import open as h5open __authors__ = ["P. Knobel"] __license__ = "MIT" -__date__ = "10/02/2017" +__date__ = "16/06/2017" logger = logging.getLogger(__name__) @@ -82,6 +82,76 @@ def _prepare_hdf5_dataset(array_like): return array +class _SafeH5FileWrite(object): + """Context manager returning a :class:`h5py.File` object. + + If this object is initialized with a file path, we open the file + and then we close it on exiting. + + If a :class:`h5py.File` instance is provided to :meth:`__init__` rather + than a path, we assume that the user is responsible for closing the + file. + + This behavior is well suited for handling h5py file in a recursive + function. The object is created in the initial call if a path is provided, + and it is closed only at the end when all the processing is finished. + """ + def __init__(self, h5file, mode="w"): + """ + + :param h5file: HDF5 file path or :class:`h5py.File` instance + :param str mode: Can be ``"r+"`` (read/write, file must exist), + ``"w"`` (write, existing file is lost), ``"w-"`` (write, fail if + exists) or ``"a"`` (read/write if exists, create otherwise). + This parameter is ignored if ``h5file`` is a file handle. + """ + self.raw_h5file = h5file + self.mode = mode + + def __enter__(self): + if not isinstance(self.raw_h5file, h5py.File): + self.h5file = h5py.File(self.raw_h5file, self.mode) + self.close_when_finished = True + else: + self.h5file = self.raw_h5file + self.close_when_finished = False + return self.h5file + + def __exit__(self, exc_type, exc_val, exc_tb): + if self.close_when_finished: + self.h5file.close() + + +class _SafeH5FileRead(object): + """Context manager returning a :class:`h5py.File` or a + :class:`silx.io.spech5.SpecH5` or a :class:`silx.io.fabioh5.File` object. + + The general behavior is the same as :class:`_SafeH5FileWrite` except + that SPEC files and all formats supported by fabio can also be opened, + but in read-only mode. + """ + def __init__(self, h5file): + """ + + :param h5file: HDF5 file path or h5py.File-like object + """ + self.raw_h5file = h5file + + def __enter__(self): + if not is_h5_file_like(self.raw_h5file): + self.h5file = h5open(self.raw_h5file) + self.close_when_finished = True + else: + self.h5file = self.raw_h5file + self.close_when_finished = False + + return self.h5file + + def __exit__(self, exc_type, exc_val, exc_tb): + if self.close_when_finished: + self.h5file.close() + + def dicttoh5(treedict, h5file, h5path='/', mode="w", overwrite_data=False, create_dataset_args=None): @@ -142,40 +212,32 @@ def dicttoh5(treedict, h5file, h5path='/', if h5py_missing: raise h5py_import_error - if not isinstance(h5file, h5py.File): - h5f = h5py.File(h5file, mode) - else: - h5f = h5file - if not h5path.endswith("/"): h5path += "/" - for key in treedict: - - if isinstance(treedict[key], dict) and len(treedict[key]): - # non-empty group: recurse - dicttoh5(treedict[key], h5f, h5path + key, - overwrite_data=overwrite_data, - create_dataset_args=create_dataset_args) + with _SafeH5FileWrite(h5file, mode=mode) as h5f: + for key in treedict: + if isinstance(treedict[key], dict) and len(treedict[key]): + # non-empty group: recurse + dicttoh5(treedict[key], h5f, h5path + key, + overwrite_data=overwrite_data, + create_dataset_args=create_dataset_args) - elif treedict[key] is None or (isinstance(treedict[key], dict) and - not len(treedict[key])): - # Create empty group - h5f.create_group(h5path + key) + elif treedict[key] is None or (isinstance(treedict[key], dict) and + not len(treedict[key])): + # Create empty group + h5f.create_group(h5path + key) - else: - ds = _prepare_hdf5_dataset(treedict[key]) - # can't apply filters on scalars (datasets with shape == () ) - if ds.shape == () or create_dataset_args is None: - h5f.create_dataset(h5path + key, - data=ds) else: - h5f.create_dataset(h5path + key, - data=ds, - **create_dataset_args) - - if isinstance(h5file, string_types): - h5f.close() + ds = _prepare_hdf5_dataset(treedict[key]) + # can't apply filters on scalars (datasets with shape == () ) + if ds.shape == () or create_dataset_args is None: + h5f.create_dataset(h5path + key, + data=ds) + else: + h5f.create_dataset(h5path + key, + data=ds, + **create_dataset_args) def _name_contains_string_in_list(name, strlist): @@ -228,26 +290,18 @@ def h5todict(h5file, path="/", exclude_names=None): if h5py_missing: raise h5py_import_error - if not is_file(h5file): - h5f = h5open(h5file) - else: - h5f = h5file - - ddict = {} - for key in h5f[path]: - if _name_contains_string_in_list(key, exclude_names): - continue - if is_group(h5f[path + "/" + key]): - ddict[key] = h5todict(h5f, - path + "/" + key, - exclude_names=exclude_names) - else: - # Convert HDF5Â dataset to numpy array - ddict[key] = h5f[path + "/" + key][...] - - if not is_file(h5file): - # close file, if we opened it - h5f.close() + with _SafeH5FileRead(h5file) as h5f: + ddict = {} + for key in h5f[path]: + if _name_contains_string_in_list(key, exclude_names): + continue + if is_group(h5f[path + "/" + key]): + ddict[key] = h5todict(h5f, + path + "/" + key, + exclude_names=exclude_names) + else: + # Convert HDF5Â dataset to numpy array + ddict[key] = h5f[path + "/" + key][...] return ddict diff --git a/silx/io/fabioh5.py b/silx/io/fabioh5.py index 092ac0c..3dfba96 100644 --- a/silx/io/fabioh5.py +++ b/silx/io/fabioh5.py @@ -28,472 +28,43 @@ .. note:: This module has a dependency on the `h5py <http://www.h5py.org/>`_ and `fabio <https://github.com/silx-kit/fabio>`_ libraries, - which are not a mandatory dependencies for `silx`. You might need - to install it if you don't already have it. + which are not mandatory dependencies for `silx`. + """ import collections -import numpy -import numbers +import datetime import logging -from silx.third_party import six - -_logger = logging.getLogger(__name__) - -try: - import fabio -except ImportError as e: - _logger.error("Module %s requires fabio", __name__) - raise e - -try: - import h5py -except ImportError as e: - _logger.error("Module %s requires h5py", __name__) - raise e - - -class Node(object): - """Main class for all fabioh5 classes. Help to manage a tree.""" - - def __init__(self, name, parent=None): - self.__parent = parent - self.__basename = name - - @property - def h5py_class(self): - """Returns the h5py classes which is mimicked by this class. It can be - one of `h5py.File, h5py.Group` or `h5py.Dataset` - - :rtype: Class - """ - raise NotImplementedError() - - @property - def parent(self): - """Returns the parent of the node. - - :rtype: Node - """ - return self.__parent - - @property - def file(self): - """Returns the file node of this node. - - :rtype: Node - """ - node = self - while node.__parent is not None: - node = node.__parent - if isinstance(node, File): - return node - else: - return None - - def _set_parent(self, parent): - """Set the parent of this node. - - It do not update the parent object. - - :param Node parent: New parent for this node - """ - self.__parent = parent - - @property - def attrs(self): - """Returns HDF5 attributes of this node. - - :rtype: dict - """ - return {} - - @property - def name(self): - """Returns the HDF5 name of this node. - """ - if self.__parent is None: - return "/" - if self.__parent.name == "/": - return "/" + self.basename - return self.__parent.name + "/" + self.basename - - @property - def basename(self): - """Returns the HDF5 basename of this node. - """ - return self.__basename - - -class Dataset(Node): - """Class which handle a numpy data as a mimic of a h5py.Dataset. - """ - - def __init__(self, name, data, parent=None, attrs=None): - self.__data = data - Node.__init__(self, name, parent) - if attrs is None: - self.__attrs = {} - else: - self.__attrs = attrs - - def _set_data(self, data): - """Set the data exposed by the dataset. - - It have to be called only one time before the data is used. It should - not be edited after use. - - :param numpy.ndarray data: Data associated to the dataset - """ - self.__data = data - - def _get_data(self): - """Returns the exposed data - - :rtype: numpy.ndarray - """ - return self.__data - - @property - def attrs(self): - """Returns HDF5 attributes of this node. - - :rtype: dict - """ - return self.__attrs - - @property - def h5py_class(self): - """Returns the h5py classes which is mimicked by this class. It can be - one of `h5py.File, h5py.Group` or `h5py.Dataset` - - :rtype: Class - """ - return h5py.Dataset - - @property - def dtype(self): - """Returns the numpy datatype exposed by this dataset. - - :rtype: numpy.dtype - """ - return self._get_data().dtype - - @property - def shape(self): - """Returns the shape of the data exposed by this dataset. - - :rtype: tuple - """ - if isinstance(self._get_data(), numpy.ndarray): - return self._get_data().shape - else: - return tuple() - - @property - def size(self): - """Returns the size of the data exposed by this dataset. - - :rtype: int - """ - if isinstance(self._get_data(), numpy.ndarray): - return self._get_data().size - else: - # It is returned as float64 1.0 by h5py - return numpy.float64(1.0) - - def __len__(self): - """Returns the size of the data exposed by this dataset. - - :rtype: int - """ - if isinstance(self._get_data(), numpy.ndarray): - return len(self._get_data()) - else: - # It is returned as float64 1.0 by h5py - raise TypeError("Attempt to take len() of scalar dataset") - - def __getitem__(self, item): - """Returns the slice of the data exposed by this dataset. - - :rtype: numpy.ndarray - """ - if not isinstance(self._get_data(), numpy.ndarray): - if item == Ellipsis: - return numpy.array(self._get_data()) - elif item == tuple(): - return self._get_data() - else: - raise ValueError("Scalar can only be reached with an ellipsis or an empty tuple") - return self._get_data().__getitem__(item) - - def __str__(self): - basename = self.name.split("/")[-1] - return '<FabIO dataset "%s": shape %s, type "%s">' % \ - (basename, self.shape, self.dtype.str) - - def __getslice__(self, i, j): - """Returns the slice of the data exposed by this dataset. - - Deprecated but still in use for python 2.7 - - :rtype: numpy.ndarray - """ - return self.__getitem__(slice(i, j, None)) - - @property - def value(self): - """Returns the data exposed by this dataset. - - Deprecated by h5py. It is prefered to use indexing `[()]`. - - :rtype: numpy.ndarray - """ - return self._get_data() - - @property - def compression(self): - """Returns compression as provided by `h5py.Dataset`. - - There is no compression.""" - return None - - @property - def compression_opts(self): - """Returns compression options as provided by `h5py.Dataset`. - - There is no compression.""" - return None - - @property - def chunks(self): - """Returns chunks as provided by `h5py.Dataset`. - - There is no chunks.""" - return None - - -class LazyLoadableDataset(Dataset): - """Abstract dataset which provide a lazy loading of the data. - - The class have to be inherited and the :meth:`_create_data` have to be - implemented to return the numpy data exposed by the dataset. This factory - is only called ones, when the data is needed. - """ - - def __init__(self, name, parent=None, attrs=None): - super(LazyLoadableDataset, self).__init__(name, None, parent, attrs=attrs) - self.__is_initialized = False - - def _create_data(self): - """ - Factory to create the data exposed by the dataset when it is needed. - - It have to be implemented to work. - - :rtype: numpy.ndarray - """ - raise NotImplementedError() - - def _get_data(self): - """Returns the data exposed by the dataset. - - Overwrite Dataset method :meth:`_get_data` to implement the lazy - loading feature. - - :rtype: numpy.ndarray - """ - if not self.__is_initialized: - data = self._create_data() - self._set_data(data) - self.__is_initialized = True - return super(LazyLoadableDataset, self)._get_data() - - -class Group(Node): - """Class which mimic a `h5py.Group`.""" - - def __init__(self, name, parent=None, attrs=None): - Node.__init__(self, name, parent) - self.__items = collections.OrderedDict() - if attrs is None: - attrs = {} - self.__attrs = attrs - - def _get_items(self): - """Returns the child items as a name-node dictionary. - - :rtype: dict - """ - return self.__items - - def add_node(self, node): - """Add a child to this group. - - :param Node node: Child to add to this group - """ - self._get_items()[node.basename] = node - node._set_parent(self) - - @property - def h5py_class(self): - """Returns the h5py classes which is mimicked by this class. - - It returns `h5py.Group` - - :rtype: Class - """ - return h5py.Group - - @property - def attrs(self): - """Returns HDF5 attributes of this node. - - :rtype: dict - """ - return self.__attrs - - def items(self): - """Returns items iterator containing name-node mapping. - - :rtype: iterator - """ - return self._get_items().items() - - def get(self, name, default=None, getclass=False, getlink=False): - """ Retrieve an item or other information. - - If getlink only is true, the returned value is always HardLink - cause this implementation do not use links. Like the original - implementation. - - :param str name: name of the item - :param object default: default value returned if the name is not found - :param bool getclass: if true, the returned object is the class of the object found - :param bool getlink: if true, links object are returned instead of the target - :return: An object, else None - :rtype: object - """ - if name not in self._get_items(): - return default - - if getlink: - node = h5py.HardLink() - else: - node = self._get_items()[name] - - if getclass: - obj = node.h5py_class - else: - obj = node - return obj - - def __len__(self): - """Returns the number of child contained in this group. - - :rtype: int - """ - return len(self._get_items()) - - def __iter__(self): - """Iterate over member names""" - for x in self._get_items().__iter__(): - yield x - - def __getitem__(self, name): - """Return a child from is name. - - :param name str: name of a member or a path throug members using '/' - separator. A '/' as a prefix access to the root item of the tree. - :rtype: Node - """ - - if name is None or name == "": - raise ValueError("No name") - - if "/" not in name: - return self._get_items()[name] - - if name.startswith("/"): - root = self - while root.parent is not None: - root = root.parent - if name == "/": - return root - return root[name[1:]] - - path = name.split("/") - result = self - for item_name in path: - if not isinstance(result, Group): - raise KeyError("Unable to open object (Component not found)") - result = result._get_items()[item_name] - - return result - - def __contains__(self, name): - """Returns true is a name is an existing child of this group. - - :rtype: bool - """ - return name in self._get_items() - - def keys(self): - return self._get_items().keys() - - -class LazyLoadableGroup(Group): - """Abstract group which provide a lazy loading of the child. - - The class have to be inherited and the :meth:`_create_child` have to be - implemented to add (:meth:`_add_node`) all child. This factory - is only called ones, when child are needed. - """ - - def __init__(self, name, parent=None, attrs=None): - Group.__init__(self, name, parent, attrs) - self.__is_initialized = False - - def _get_items(self): - """Returns internal structure which contains child. - - It overwrite method :meth:`_get_items` to implement the lazy - loading feature. +import numbers - :rtype: dict - """ - if not self.__is_initialized: - self.__is_initialized = True - self._create_child() - return Group._get_items(self) +import fabio +import numpy - def _create_child(self): - """ - Factory to create the child contained by the group when it is needed. +from . import commonh5 +from silx.third_party import six +from silx import version as silx_version - It have to be implemented to work. - """ - raise NotImplementedError() +_logger = logging.getLogger(__name__) -class FrameData(LazyLoadableDataset): +class FrameData(commonh5.LazyLoadableDataset): """Expose a cube of image from a Fabio file using `FabioReader` as cache.""" def __init__(self, name, fabio_reader, parent=None): attrs = {"interpretation": "image"} - LazyLoadableDataset.__init__(self, name, parent, attrs=attrs) + commonh5.LazyLoadableDataset.__init__(self, name, parent, attrs=attrs) self.__fabio_reader = fabio_reader def _create_data(self): return self.__fabio_reader.get_data() -class RawHeaderData(LazyLoadableDataset): +class RawHeaderData(commonh5.LazyLoadableDataset): """Lazy loadable raw header""" def __init__(self, name, fabio_file, parent=None): - LazyLoadableDataset.__init__(self, name, parent) + commonh5.LazyLoadableDataset.__init__(self, name, parent) self.__fabio_file = fabio_file def _create_data(self): @@ -510,18 +81,18 @@ class RawHeaderData(LazyLoadableDataset): for key, value in header.items(): data.append("%s: %s" % (str(key), str(value))) - headers.append(u"\n".join(data)) + headers.append(u"\n".join(data).encode("utf-8")) # create the header list - return numpy.array(headers) + return numpy.array(headers, dtype=numpy.string_) -class MetadataGroup(LazyLoadableGroup): +class MetadataGroup(commonh5.LazyLoadableGroup): """Abstract class for groups containing a reference to a fabio image. """ def __init__(self, name, metadata_reader, kind, parent=None, attrs=None): - LazyLoadableGroup.__init__(self, name, parent, attrs) + commonh5.LazyLoadableGroup.__init__(self, name, parent, attrs) self.__metadata_reader = metadata_reader self.__kind = kind @@ -529,7 +100,7 @@ class MetadataGroup(LazyLoadableGroup): keys = self.__metadata_reader.get_keys(self.__kind) for name in keys: data = self.__metadata_reader.get_value(self.__kind, name) - dataset = Dataset(name, data) + dataset = commonh5.Dataset(name, data) self.add_node(dataset) @property @@ -537,14 +108,14 @@ class MetadataGroup(LazyLoadableGroup): return self.__metadata_reader -class DetectorGroup(LazyLoadableGroup): +class DetectorGroup(commonh5.LazyLoadableGroup): """Define the detector group (sub group of instrument) using Fabio data. """ def __init__(self, name, fabio_reader, parent=None, attrs=None): if attrs is None: attrs = {"NX_class": "NXdetector"} - LazyLoadableGroup.__init__(self, name, parent, attrs) + commonh5.LazyLoadableGroup.__init__(self, name, parent, attrs) self.__fabio_reader = fabio_reader def _create_child(self): @@ -558,57 +129,56 @@ class DetectorGroup(LazyLoadableGroup): self.add_node(others) -class ImageGroup(LazyLoadableGroup): +class ImageGroup(commonh5.LazyLoadableGroup): """Define the image group (sub group of measurement) using Fabio data. """ def __init__(self, name, fabio_reader, parent=None, attrs=None): - LazyLoadableGroup.__init__(self, name, parent, attrs) + commonh5.LazyLoadableGroup.__init__(self, name, parent, attrs) self.__fabio_reader = fabio_reader def _create_child(self): - data = FrameData("data", self.__fabio_reader) + basepath = self.parent.parent.name + data = commonh5.SoftLink("data", path=basepath + "/instrument/detector_0/data") self.add_node(data) - - # TODO detector should be a real soft-link - detector = DetectorGroup("info", self.__fabio_reader) + detector = commonh5.SoftLink("info", path=basepath + "/instrument/detector_0") self.add_node(detector) -class SampleGroup(LazyLoadableGroup): +class SampleGroup(commonh5.LazyLoadableGroup): """Define the image group (sub group of measurement) using Fabio data. """ def __init__(self, name, fabio_reader, parent=None): attrs = {"NXclass": "NXsample"} - LazyLoadableGroup.__init__(self, name, parent, attrs) + commonh5.LazyLoadableGroup.__init__(self, name, parent, attrs) self.__fabio_reader = fabio_reader def _create_child(self): if self.__fabio_reader.has_ub_matrix(): scalar = {"interpretation": "scalar"} data = self.__fabio_reader.get_unit_cell_abc() - data = Dataset("unit_cell_abc", data, attrs=scalar) + data = commonh5.Dataset("unit_cell_abc", data, attrs=scalar) self.add_node(data) unit_cell_data = numpy.zeros((1, 6), numpy.float32) unit_cell_data[0, :3] = data data = self.__fabio_reader.get_unit_cell_alphabetagamma() - data = Dataset("unit_cell_alphabetagamma", data, attrs=scalar) + data = commonh5.Dataset("unit_cell_alphabetagamma", data, attrs=scalar) self.add_node(data) unit_cell_data[0, 3:] = data - data = Dataset("unit_cell", unit_cell_data, attrs=scalar) + data = commonh5.Dataset("unit_cell", unit_cell_data, attrs=scalar) self.add_node(data) data = self.__fabio_reader.get_ub_matrix() - data = Dataset("ub_matrix", data, attrs=scalar) + data = commonh5.Dataset("ub_matrix", data, attrs=scalar) self.add_node(data) -class MeasurementGroup(LazyLoadableGroup): +class MeasurementGroup(commonh5.LazyLoadableGroup): """Define the measurement group for fabio file. """ def __init__(self, name, fabio_reader, parent=None, attrs=None): - LazyLoadableGroup.__init__(self, name, parent, attrs) + commonh5.LazyLoadableGroup.__init__(self, name, parent, attrs) self.__fabio_reader = fabio_reader def _create_child(self): @@ -628,7 +198,7 @@ class MeasurementGroup(LazyLoadableGroup): # add all counters for name in keys: data = self.__fabio_reader.get_value(FabioReader.COUNTER, name) - dataset = Dataset(name, data) + dataset = commonh5.Dataset(name, data) self.add_node(dataset) @@ -667,22 +237,29 @@ class FabioReader(object): image = self.__fabio_file.getframe(frame).data images.append(image) + # returns the data without extra dim in case of single frame + if len(images) == 1: + return images[0] + # get the max size - max_shape = [0, 0] + max_dim = max([i.ndim for i in images]) + max_shape = [0] * max_dim for image in images: - if image.shape[0] > max_shape[0]: - max_shape[0] = image.shape[0] - if image.shape[1] > max_shape[1]: - max_shape[1] = image.shape[1] + for dim in range(image.ndim): + if image.shape[dim] > max_shape[dim]: + max_shape[dim] = image.shape[dim] max_shape = tuple(max_shape) # fix smallest images for index, image in enumerate(images): if image.shape == max_shape: continue - right_image = numpy.zeros(max_shape) - right_image[0:image.shape[0], 0:image.shape[1]] = image - images[index] = right_image + location = [slice(0, i) for i in image.shape] + while len(location) < max_dim: + location.append(0) + normalized_image = numpy.zeros(max_shape, dtype=image.dtype) + normalized_image[location] = image + images[index] = normalized_image # create a cube return numpy.array(images) @@ -1058,7 +635,7 @@ class EdfFabioReader(FabioReader): return self.__ub_matrix -class File(Group): +class File(commonh5.File): """Class which handle a fabio image as a mimick of a h5py.File. """ @@ -1071,7 +648,12 @@ class File(Group): self.__must_be_closed = True elif fabio_image is not None: self.__fabio_image = fabio_image - Group.__init__(self, name="", parent=None, attrs={"NX_class": "NXroot"}) + file_name = self.__fabio_image.filename + attrs = {"NX_class": "NXroot", + "file_time": datetime.datetime.now().isoformat(), + "file_name": file_name, + "creator": "silx %s" % silx_version} + commonh5.File.__init__(self, name=file_name, attrs=attrs) self.__fabio_reader = self.create_fabio_reader(self.__fabio_image) scan = self.create_scan_group(self.__fabio_image, self.__fabio_reader) self.add_node(scan) @@ -1081,13 +663,13 @@ class File(Group): :param FabioImage fabio_image: A Fabio image :param FabioReader fabio_reader: A reader for the Fabio image - :rtype: Group + :rtype: commonh5.Group """ - scan = Group("scan_0", attrs={"NX_class": "NXentry"}) - instrument = Group("instrument", attrs={"NX_class": "NXinstrument"}) + scan = commonh5.Group("scan_0", attrs={"NX_class": "NXentry"}) + instrument = commonh5.Group("instrument", attrs={"NX_class": "NXinstrument"}) measurement = MeasurementGroup("measurement", fabio_reader, attrs={"NX_class": "NXcollection"}) - file_ = Group("file", attrs={"NX_class": "NXcollection"}) + file_ = commonh5.Group("file", attrs={"NX_class": "NXcollection"}) positioners = MetadataGroup("positioners", fabio_reader, FabioReader.POSITIONER, attrs={"NX_class": "NXpositioner"}) raw_header = RawHeaderData("scan_header", fabio_image, self) detector = DetectorGroup("detector_0", fabio_reader) @@ -1115,29 +697,6 @@ class File(Group): metadata = FabioReader(fabio_file) return metadata - @property - def h5py_class(self): - return h5py.File - - @property - def filename(self): - return self.__fabio_image.filename - - def __enter__(self): - return self - - def __exit__(self, type, value, tb): # pylint: disable=W0622 - """Called at the end of a `with` statement. - - It will close the internal FabioImage only if the FabioImage was - created by the class itself. The reference to the FabioImage is anyway - broken. - """ - if self.__must_be_closed: - self.close() - else: - self.__fabio_image = None - def close(self): """Close the object, and free up associated resources. @@ -1146,6 +705,8 @@ class File(Group): After calling this method, attempts to use the object may fail. """ - # It looks like there is no close on FabioImage - # self.__fabio_image.close() + if self.__must_be_closed: + # It looks like there is no close on FabioImage + # self.__fabio_image.close() + pass self.__fabio_image = None diff --git a/silx/io/nxdata.py b/silx/io/nxdata.py index c0e53fc..977721f 100644 --- a/silx/io/nxdata.py +++ b/silx/io/nxdata.py @@ -55,7 +55,7 @@ def _nxdata_warning(msg): _logger.warning("NXdata warning: " + msg) -def _get_attr(item, attr_name, default=None): +def get_attr_as_string(item, attr_name, default=None): """Return item.attrs[attr_name]. If it is a byte-string or an array of byte-strings, return it as a default python string. @@ -72,12 +72,12 @@ def _get_attr(item, attr_name, default=None): if six.PY3: if hasattr(attr, "decode"): # byte-string - return attr.decode("ascii") + return attr.decode("utf-8") elif isinstance(attr, numpy.ndarray) and hasattr(attr[0], "decode"): - # array of byte-strinqs - return [element.decode("ascii") for element in attr] + # array of byte-strings + return [element.decode("utf-8") for element in attr] else: - # attr is not a byte-strinq + # attr is not a byte-string return attr @@ -97,65 +97,65 @@ def is_valid_nxdata(group): # noqa """ if not is_group(group): raise TypeError("group must be a h5py-like group") - if _get_attr(group, "NX_class") != "NXdata": + if get_attr_as_string(group, "NX_class") != "NXdata": return False if "signal" not in group.attrs: _logger.warning("NXdata group does not define a signal attr.") return False - signal_name = _get_attr(group, "signal") + signal_name = get_attr_as_string(group, "signal") if signal_name not in group or not is_dataset(group[signal_name]): _logger.warning( - "Cannot find signal dataset '%s' in NXdata group" % signal_name) + "Cannot find signal dataset '%s' in NXdata group" % signal_name) return False ndim = len(group[signal_name].shape) if "axes" in group.attrs: - axes_names = _get_attr(group, "axes") + axes_names = get_attr_as_string(group, "axes") if isinstance(axes_names, str): axes_names = [axes_names] if 1 < ndim < len(axes_names): # ndim = 1 and several axes could be a scatter _nxdata_warning( - "More @axes defined than there are " + - "signal dimensions: " + - "%d axes, %d dimensions." % (len(axes_names), ndim)) + "More @axes defined than there are " + + "signal dimensions: " + + "%d axes, %d dimensions." % (len(axes_names), ndim)) return False # case of less axes than dimensions: number of axes must match # dimensionality defined by @interpretation if ndim > len(axes_names): - interpretation = _get_attr(group[signal_name], "interpretation", None) + interpretation = get_attr_as_string(group[signal_name], "interpretation") if interpretation is None: - interpretation = _get_attr(group, "interpretation", None) + interpretation = get_attr_as_string(group, "interpretation") if interpretation is None: _nxdata_warning("No @interpretation and not enough" + - " @axes defined.") + " @axes defined.") return False if interpretation not in _INTERPDIM: _nxdata_warning("Unrecognized @interpretation=" + interpretation + - " for data with wrong number of defined @axes.") + " for data with wrong number of defined @axes.") return False if len(axes_names) != _INTERPDIM[interpretation]: _nxdata_warning( - "%d-D signal with @interpretation=%s " % (ndim, interpretation) + - "must define %d or %d axes." % (ndim, _INTERPDIM[interpretation])) + "%d-D signal with @interpretation=%s " % (ndim, interpretation) + + "must define %d or %d axes." % (ndim, _INTERPDIM[interpretation])) return False # Test consistency of @uncertainties - uncertainties_names = _get_attr(group, "uncertainties") + uncertainties_names = get_attr_as_string(group, "uncertainties") if uncertainties_names is None: - uncertainties_names = _get_attr(group[signal_name], "uncertainties") + uncertainties_names = get_attr_as_string(group[signal_name], "uncertainties") if isinstance(uncertainties_names, str): uncertainties_names = [uncertainties_names] if uncertainties_names is not None: if len(uncertainties_names) != len(axes_names): _nxdata_warning("@uncertainties does not define the same " + - "number of fields than @axes") + "number of fields than @axes") return False # Test individual axes @@ -180,22 +180,22 @@ def is_valid_nxdata(group): # noqa # size is exactly the signal's size (weird n-d scatter) if axis_size != signal_size: _nxdata_warning("Axis %s is not a 1D dataset" % axis_name + - " and its shape does not match the signal's shape") + " and its shape does not match the signal's shape") return False axis_len = axis_size else: # for a 1-d axis, - fg_idx = _get_attr(group[axis_name], "first_good", 0) - lg_idx = _get_attr(group[axis_name], "last_good", len(group[axis_name]) - 1) + fg_idx = group[axis_name].attrs.get("first_good", 0) + lg_idx = group[axis_name].attrs.get("last_good", len(group[axis_name]) - 1) axis_len = lg_idx + 1 - fg_idx if axis_len != signal_size: if axis_len not in group[signal_name].shape + (1, 2): _nxdata_warning( - "Axis %s number of elements does not " % axis_name + - "correspond to the length of any signal dimension," - " it does not appear to be a constant or a linear calibration," + - " and this does not seem to be a scatter plot.") + "Axis %s number of elements does not " % axis_name + + "correspond to the length of any signal dimension," + " it does not appear to be a constant or a linear calibration," + + " and this does not seem to be a scatter plot.") return False elif axis_len in (1, 2): polynomial_axes_names.append(axis_name) @@ -203,9 +203,9 @@ def is_valid_nxdata(group): # noqa else: if not is_scatter: _nxdata_warning( - "Axis %s number of elements is equal " % axis_name + - "to the length of the signal, but this does not seem" + - " to be a scatter (other axes have different sizes)") + "Axis %s number of elements is equal " % axis_name + + "to the length of the signal, but this does not seem" + + " to be a scatter (other axes have different sizes)") return False # Test individual uncertainties @@ -223,7 +223,7 @@ def is_valid_nxdata(group): # noqa if "errors" in group and is_dataset(group["errors"]): if group["errors"].shape != group[signal_name].shape: _nxdata_warning("Dataset containing standard deviations must " + - "have the same dimensions as the signal.") + "have the same dimensions as the signal.") return False return True @@ -245,7 +245,7 @@ class NXdata(object): """h5py-like group object compliant with NeXus NXdata specification. """ - self.signal = self.group[self.group.attrs["signal"]] + self.signal = self.group[get_attr_as_string(self.group, "signal")] """Signal dataset in this NXdata group. """ @@ -268,7 +268,7 @@ class NXdata(object): # check if axis dataset defines @long_name for i, dsname in enumerate(self.axes_dataset_names): if dsname is not None and "long_name" in self.group[dsname].attrs: - self.axes_names.append(self.group[dsname].attrs["long_name"]) + self.axes_names.append(get_attr_as_string(self.group[dsname], "long_name")) else: self.axes_names.append(dsname) @@ -303,9 +303,9 @@ class NXdata(object): # "rgba-image", "hsla-image", "cmyk-image" # TODO "vertex"] - interpretation = _get_attr(self.signal, "interpretation", None) + interpretation = get_attr_as_string(self.signal, "interpretation") if interpretation is None: - interpretation = _get_attr(self.group, "interpretation", None) + interpretation = get_attr_as_string(self.group, "interpretation") if interpretation not in allowed_interpretations: _logger.warning("Interpretation %s is not valid." % interpretation + @@ -347,7 +347,7 @@ class NXdata(object): # use cache return self._axes ndims = len(self.signal.shape) - axes_names = _get_attr(self.group, "axes") + axes_names = get_attr_as_string(self.group, "axes") interpretation = self.interpretation if axes_names is None: @@ -386,8 +386,8 @@ class NXdata(object): continue if "first_good" not in axis.attrs and "last_good" not in axis.attrs: continue - fg_idx = _get_attr(axis, "first_good") or 0 - lg_idx = _get_attr(axis, "last_good") or (len(axis) - 1) + fg_idx = axis.attrs.get("first_good", 0) + lg_idx = axis.attrs.get("last_good", len(axis) - 1) axes[i] = axis[fg_idx:lg_idx + 1] self._axes = axes @@ -403,9 +403,9 @@ class NXdata(object): "." in that position in the *@axes* array), `None` is inserted in the output list in its position. """ - axes_dataset_names = _get_attr(self.group, "axes") + axes_dataset_names = get_attr_as_string(self.group, "axes") if axes_dataset_names is None: - axes_dataset_names = _get_attr(self.group, "axes") + axes_dataset_names = get_attr_as_string(self.group, "axes") ndims = len(self.signal.shape) if axes_dataset_names is None: @@ -415,6 +415,8 @@ class NXdata(object): axes_dataset_names = [axes_dataset_names] for i, axis_name in enumerate(axes_dataset_names): + if hasattr(axis_name, "decode"): + axis_name = axis_name.decode() if axis_name == ".": axes_dataset_names[i] = None @@ -442,10 +444,13 @@ class NXdata(object): :return: Dataset with axis errors, or None :raise: KeyError if this group does not contain a dataset named axis_name """ + # ensure axis_name is decoded, before comparing it with decoded attributes + if hasattr(axis_name, "decode"): + axis_name = axis_name.decode("utf-8") if axis_name not in self.group: # tolerate axis_name given as @long_name for item in self.group: - long_name = _get_attr(self.group[item], "long_name") + long_name = get_attr_as_string(self.group[item], "long_name") if long_name is not None and long_name == axis_name: axis_name = item break @@ -455,37 +460,40 @@ class NXdata(object): len_axis = len(self.group[axis_name]) - fg_idx = _get_attr(self.group[axis_name], "first_good", 0) - lg_idx = _get_attr(self.group[axis_name], "last_good", len_axis - 1) + fg_idx = self.group[axis_name].attrs.get("first_good", 0) + lg_idx = self.group[axis_name].attrs.get("last_good", len_axis - 1) # case of axisname_errors dataset present errors_name = axis_name + "_errors" if errors_name in self.group and is_dataset(self.group[errors_name]): - if fg_idx != 0 or lg_idx != (len_axis-1): + if fg_idx != 0 or lg_idx != (len_axis - 1): return self.group[errors_name][fg_idx:lg_idx + 1] else: return self.group[errors_name] # case of uncertainties dataset name provided in @uncertainties - uncertainties_names = _get_attr(self.group, "uncertainties") + uncertainties_names = get_attr_as_string(self.group, "uncertainties") if uncertainties_names is None: - uncertainties_names = _get_attr(self.signal, "uncertainties") + uncertainties_names = get_attr_as_string(self.signal, "uncertainties") if isinstance(uncertainties_names, str): uncertainties_names = [uncertainties_names] if uncertainties_names is not None: # take the uncertainty with the same index as the axis in @axes - axes_ds_names = _get_attr(self.group, "axes") + axes_ds_names = get_attr_as_string(self.group, "axes") if axes_ds_names is None: - axes_ds_names = _get_attr(self.signal, "axes") + axes_ds_names = get_attr_as_string(self.signal, "axes") if isinstance(axes_ds_names, str): axes_ds_names = [axes_ds_names] - elif not isinstance(axes_ds_names, list): - # transform numpy.ndarray(dtype('S21')) into list(str) - axes_ds_names = map(str, axes_ds_names) + elif isinstance(axes_ds_names, numpy.ndarray): + # transform numpy.ndarray into list + axes_ds_names = list(axes_ds_names) + assert isinstance(axes_ds_names, list) + if hasattr(axes_ds_names[0], "decode"): + axes_ds_names = [ax_name.decode("utf-8") for ax_name in axes_ds_names] if axis_name not in axes_ds_names: raise KeyError("group attr @axes does not mention a dataset " + "named '%s'" % axis_name) errors = self.group[uncertainties_names[list(axes_ds_names).index(axis_name)]] - if fg_idx == 0 and lg_idx == (len_axis-1): + if fg_idx == 0 and lg_idx == (len_axis - 1): return errors # dataset else: return errors[fg_idx:lg_idx + 1] # numpy array diff --git a/silx/io/rawh5.py b/silx/io/rawh5.py new file mode 100644 index 0000000..ceabbdb --- /dev/null +++ b/silx/io/rawh5.py @@ -0,0 +1,71 @@ +# coding: utf-8 +# /*########################################################################## +# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +# THE SOFTWARE. +# +# ############################################################################*/ +""" +This module contains wrapper from file format to h5py. The exposed layout is +as close as possible to the original file format. +""" +import numpy +from . import commonh5 +import logging + +__authors__ = ["V. Valls"] +__license__ = "MIT" +__date__ = "21/09/2017" + + +_logger = logging.getLogger(__name__) + + +class _FreeDataset(commonh5.Dataset): + + def _check_data(self, data): + """Release the constriants checked on types cause we can reach more + types than the one available on h5py, and it is not supposed to be + converted into h5py.""" + chartype = data.dtype.char + if chartype in ["U", "O"]: + msg = "Dataset '%s' uses an unsupported type '%s'." + msg = msg % (self.name, data.dtype) + _logger.warning(msg) + + +class NumpyFile(commonh5.File): + """ + Expose a numpy file `npy`, or `npz` as an h5py.File-like. + + :param str name: Filename to load + """ + def __init__(self, name=None): + commonh5.File.__init__(self, name=name, mode="w") + np_file = numpy.load(name) + if hasattr(np_file, "close"): + # For npz (created using by numpy.savez, numpy.savez_compressed) + for key, value in np_file.items(): + self[key] = _FreeDataset(None, data=value) + np_file.close() + else: + # For npy (created using numpy.save) + value = np_file + dataset = _FreeDataset("data", data=value) + self.add_node(dataset) diff --git a/silx/io/setup.py b/silx/io/setup.py index 3483bcb..971d358 100644 --- a/silx/io/setup.py +++ b/silx/io/setup.py @@ -4,7 +4,7 @@ # # /*########################################################################## # -# Copyright (c) 2016 European Synchrotron Radiation Facility +# Copyright (c) 2016-2017 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -71,7 +71,7 @@ def configuration(parent_package='', top_path=None): srcfiles = ['sfheader', 'sfinit', 'sflists', 'sfdata', 'sfindex', 'sflabel', 'sfmca', 'sftools', 'locale_management'] sources = [os.path.join('specfile', 'src', ffile + '.c') for ffile in srcfiles] - sources.append(os.path.join('specfile', 'specfile.pyx')) + sources.append('specfile.pyx') config.add_extension('specfile', sources=sources, diff --git a/silx/io/specfile/specfile.c b/silx/io/specfile.c index 17e3eb2..e244f3d 100644 --- a/silx/io/specfile/specfile.c +++ b/silx/io/specfile.c @@ -1,28 +1,40 @@ -/* Generated by Cython 0.21.1 */ +/* Generated by Cython 0.25.2 */ + +/* BEGIN: Cython Metadata +{ + "distutils": { + "define_macros": [ + [ + "SPECFILE_POSIX", + null + ] + ], + "depends": [ + "/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h", + "/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ufuncobject.h", + "silx/io/specfile/include/SpecFileCython.h" + ], + "include_dirs": [ + "silx/io/specfile/include", + "/usr/lib/python2.7/dist-packages/numpy/core/include" + ], + "language": "c" + }, + "module_name": "silx.io.specfile" +} +END: Cython Metadata */ #define PY_SSIZE_T_CLEAN -#ifndef CYTHON_USE_PYLONG_INTERNALS -#ifdef PYLONG_BITS_IN_DIGIT -#define CYTHON_USE_PYLONG_INTERNALS 0 -#else -#include "pyconfig.h" -#ifdef PYLONG_BITS_IN_DIGIT -#define CYTHON_USE_PYLONG_INTERNALS 1 -#else -#define CYTHON_USE_PYLONG_INTERNALS 0 -#endif -#endif -#endif #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_21_1" +#define CYTHON_ABI "0_25_2" #include <stddef.h> #ifndef offsetof -#define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) + #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall @@ -41,6 +53,11 @@ #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif +#ifndef HAVE_LONG_LONG + #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000) + #define HAVE_LONG_LONG + #endif +#endif #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif @@ -48,63 +65,214 @@ #define Py_HUGE_VAL HUGE_VAL #endif #ifdef PYPY_VERSION -#define CYTHON_COMPILING_IN_PYPY 1 -#define CYTHON_COMPILING_IN_CPYTHON 0 + #define CYTHON_COMPILING_IN_PYPY 1 + #define CYTHON_COMPILING_IN_PYSTON 0 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #undef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 0 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #undef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 0 + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #undef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 1 + #undef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 0 + #undef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 0 + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 +#elif defined(PYSTON_VERSION) + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_PYSTON 1 + #define CYTHON_COMPILING_IN_CPYTHON 0 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #undef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 0 + #ifndef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 1 + #endif + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #ifndef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 0 + #endif + #ifndef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 1 + #endif + #ifndef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 1 + #endif + #undef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 0 + #undef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 0 #else -#define CYTHON_COMPILING_IN_PYPY 0 -#define CYTHON_COMPILING_IN_CPYTHON 1 + #define CYTHON_COMPILING_IN_PYPY 0 + #define CYTHON_COMPILING_IN_PYSTON 0 + #define CYTHON_COMPILING_IN_CPYTHON 1 + #ifndef CYTHON_USE_TYPE_SLOTS + #define CYTHON_USE_TYPE_SLOTS 1 + #endif + #if PY_MAJOR_VERSION < 3 + #undef CYTHON_USE_ASYNC_SLOTS + #define CYTHON_USE_ASYNC_SLOTS 0 + #elif !defined(CYTHON_USE_ASYNC_SLOTS) + #define CYTHON_USE_ASYNC_SLOTS 1 + #endif + #if PY_VERSION_HEX < 0x02070000 + #undef CYTHON_USE_PYLONG_INTERNALS + #define CYTHON_USE_PYLONG_INTERNALS 0 + #elif !defined(CYTHON_USE_PYLONG_INTERNALS) + #define CYTHON_USE_PYLONG_INTERNALS 1 + #endif + #ifndef CYTHON_USE_PYLIST_INTERNALS + #define CYTHON_USE_PYLIST_INTERNALS 1 + #endif + #ifndef CYTHON_USE_UNICODE_INTERNALS + #define CYTHON_USE_UNICODE_INTERNALS 1 + #endif + #if PY_VERSION_HEX < 0x030300F0 + #undef CYTHON_USE_UNICODE_WRITER + #define CYTHON_USE_UNICODE_WRITER 0 + #elif !defined(CYTHON_USE_UNICODE_WRITER) + #define CYTHON_USE_UNICODE_WRITER 1 + #endif + #ifndef CYTHON_AVOID_BORROWED_REFS + #define CYTHON_AVOID_BORROWED_REFS 0 + #endif + #ifndef CYTHON_ASSUME_SAFE_MACROS + #define CYTHON_ASSUME_SAFE_MACROS 1 + #endif + #ifndef CYTHON_UNPACK_METHODS + #define CYTHON_UNPACK_METHODS 1 + #endif + #ifndef CYTHON_FAST_THREAD_STATE + #define CYTHON_FAST_THREAD_STATE 1 + #endif + #ifndef CYTHON_FAST_PYCALL + #define CYTHON_FAST_PYCALL 1 + #endif #endif -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 -#define Py_OptimizeFlag 0 +#if !defined(CYTHON_FAST_PYCCALL) +#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) +#endif +#if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" + #undef SHIFT + #undef BASE + #undef MASK +#endif +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) + #define Py_OptimizeFlag 0 #endif #define __PYX_BUILD_PY_SSIZE_T "n" #define CYTHON_FORMAT_SSIZE_T "z" #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #define __Pyx_DefaultClassType PyClass_Type #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #define __Pyx_DefaultClassType PyType_Type #endif -#if PY_MAJOR_VERSION >= 3 +#ifndef Py_TPFLAGS_CHECKTYPES #define Py_TPFLAGS_CHECKTYPES 0 +#endif +#ifndef Py_TPFLAGS_HAVE_INDEX #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#ifndef Py_TPFLAGS_HAVE_NEWBUFFER #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif -#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE) +#ifndef Py_TPFLAGS_HAVE_FINALIZE #define Py_TPFLAGS_HAVE_FINALIZE 0 #endif +#ifndef METH_FASTCALL + #define METH_FASTCALL 0x80 + typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args, + Py_ssize_t nargs, PyObject *kwnames); +#else + #define __Pyx_PyCFunctionFast _PyCFunctionFast +#endif +#if CYTHON_FAST_PYCCALL +#define __Pyx_PyFastCFunction_Check(func)\ + ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST))))) +#else +#define __Pyx_PyFastCFunction_Check(func) 0 +#endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ 0 : _PyUnicode_Ready((PyObject *)(op))) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) + #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) #else #define CYTHON_PEP393_ENABLED 0 + #define PyUnicode_1BYTE_KIND 1 + #define PyUnicode_2BYTE_KIND 2 + #define PyUnicode_4BYTE_KIND 4 #define __Pyx_PyUnicode_READY(op) (0) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) + #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) #endif #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) - #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s) #else #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) - #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) + #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) + #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) + #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) +#endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) + #define PyObject_Malloc(s) PyMem_Malloc(s) + #define PyObject_Free(p) PyMem_Free(p) + #define PyObject_Realloc(p) PyMem_Realloc(p) +#endif +#if CYTHON_COMPILING_IN_PYSTON + #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) + #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) +#else + #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) + #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) #endif #define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) #define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) @@ -113,6 +281,9 @@ #else #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) #endif +#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII) + #define PyObject_ASCII(o) PyObject_Repr(o) +#endif #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject @@ -131,6 +302,7 @@ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) +#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) #if PY_MAJOR_VERSION >= 3 #define PyIntObject PyLongObject #define PyInt_Type PyLong_Type @@ -169,16 +341,20 @@ #else #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) #endif -#ifndef CYTHON_INLINE - #if defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline +#if CYTHON_USE_ASYNC_SLOTS + #if PY_VERSION_HEX >= 0x030500B1 + #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods + #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) #else - #define CYTHON_INLINE + typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; + } __Pyx_PyAsyncMethodsStruct; + #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) #endif +#else + #define __Pyx_PyType_AsAsync(obj) NULL #endif #ifndef CYTHON_RESTRICT #if defined(__GNUC__) @@ -191,26 +367,74 @@ #define CYTHON_RESTRICT #endif #endif +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +#ifndef CYTHON_MAYBE_UNUSED_VAR +# if defined(__cplusplus) + template<class T> void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } +# else +# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) +# endif +#endif +#ifndef CYTHON_NCP_UNUSED +# if CYTHON_COMPILING_IN_CPYTHON +# define CYTHON_NCP_UNUSED +# else +# define CYTHON_NCP_UNUSED CYTHON_UNUSED +# endif +#endif +#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) + +#ifndef CYTHON_INLINE + #if defined(__clang__) + #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) + #elif defined(__GNUC__) + #define CYTHON_INLINE __inline__ + #elif defined(_MSC_VER) + #define CYTHON_INLINE __inline + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_INLINE inline + #else + #define CYTHON_INLINE + #endif +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) + #define _USE_MATH_DEFINES +#endif +#include <math.h> #ifdef NAN #define __PYX_NAN() ((float) NAN) #else static CYTHON_INLINE float __PYX_NAN() { - /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and - a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is - a quiet NaN. */ float value; memset(&value, 0xFF, sizeof(value)); return value; } #endif -#ifdef __cplusplus -template<typename T> -void __Pyx_call_destructor(T* x) { - x->~T(); -} +#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL) +#define __Pyx_truncl trunc +#else +#define __Pyx_truncl truncl #endif +#define __PYX_ERR(f_index, lineno, Ln_error) \ +{ \ + __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \ +} + #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) @@ -227,15 +451,11 @@ void __Pyx_call_destructor(T* x) { #endif #endif -#if defined(WIN32) || defined(MS_WINDOWS) -#define _USE_MATH_DEFINES -#endif -#include <math.h> -#define __PYX_HAVE__specfile -#define __PYX_HAVE_API__specfile -#include "string.h" -#include "stdio.h" -#include "stdlib.h" +#define __PYX_HAVE__silx__io__specfile +#define __PYX_HAVE_API__silx__io__specfile +#include <string.h> +#include <stdio.h> +#include <stdlib.h> #include "numpy/arrayobject.h" #include "numpy/ufuncobject.h" #include "SpecFileCython.h" @@ -247,20 +467,7 @@ void __Pyx_call_destructor(T* x) { #define CYTHON_WITHOUT_ASSERTIONS #endif -#ifndef CYTHON_UNUSED -# if defined(__GNUC__) -# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -#endif -typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; +typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; #define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 @@ -268,16 +475,34 @@ typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; #define __PYX_DEFAULT_STRING_ENCODING "" #define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString #define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize -#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \ - (sizeof(type) < sizeof(Py_ssize_t)) || \ - (sizeof(type) > sizeof(Py_ssize_t) && \ - likely(v < (type)PY_SSIZE_T_MAX || \ - v == (type)PY_SSIZE_T_MAX) && \ - (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \ - v == (type)PY_SSIZE_T_MIN))) || \ - (sizeof(type) == sizeof(Py_ssize_t) && \ - (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \ +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ + (sizeof(type) < sizeof(Py_ssize_t)) ||\ + (sizeof(type) > sizeof(Py_ssize_t) &&\ + likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX) &&\ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ + v == (type)PY_SSIZE_T_MIN))) ||\ + (sizeof(type) == sizeof(Py_ssize_t) &&\ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ v == (type)PY_SSIZE_T_MAX))) ) +#if defined (__cplusplus) && __cplusplus >= 201103L + #include <cstdlib> + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (_MSC_VER) && defined (_M_X64) + #define __Pyx_sst_abs(value) _abs64(value) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); #define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) @@ -294,11 +519,11 @@ static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); #endif #define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) #define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s) -#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s) -#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s) -#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s) -#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s) +#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) #if PY_MAJOR_VERSION < 3 static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { @@ -312,18 +537,25 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) #define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) #define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode -#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) +#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) +#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); -static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); -#if CYTHON_COMPILING_IN_CPYTHON +#if CYTHON_ASSUME_SAFE_MACROS #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #else #define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) #endif #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION >= 3 +#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) +#else +#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) +#endif +#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII static int __Pyx_sys_getdefaultencoding_not_ascii; static int __Pyx_init_sys_getdefaultencoding_params(void) { @@ -334,7 +566,7 @@ static int __Pyx_init_sys_getdefaultencoding_params(void) { const char* default_encoding_c; sys = PyImport_ImportModule("sys"); if (!sys) goto bad; - default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); Py_DECREF(sys); if (!default_encoding) goto bad; default_encoding_c = PyBytes_AsString(default_encoding); @@ -414,11 +646,13 @@ static PyObject *__pyx_d; static PyObject *__pyx_b; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; +static PyObject *__pyx_empty_unicode; static int __pyx_lineno; static int __pyx_clineno = 0; static const char * __pyx_cfilenm= __FILE__; static const char *__pyx_filename; +/* Header.proto */ #if !defined(CYTHON_CCOMPLEX) #if defined(__cplusplus) #define CYTHON_CCOMPLEX 1 @@ -442,12 +676,12 @@ static const char *__pyx_filename; static const char *__pyx_f[] = { - "specfile.pyx", + "silx/io/specfile.pyx", "__init__.pxd", "type.pxd", }; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":723 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":725 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -456,7 +690,7 @@ static const char *__pyx_f[] = { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":724 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -465,7 +699,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":725 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":727 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -474,7 +708,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":728 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -483,7 +717,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":732 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -492,7 +726,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -501,7 +735,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":734 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -510,7 +744,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":735 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -519,7 +753,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":739 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -528,7 +762,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":740 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -537,7 +771,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":747 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":749 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -546,7 +780,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":748 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":750 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -555,7 +789,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":749 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -564,7 +798,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":753 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -573,7 +807,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":752 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":754 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -582,7 +816,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":753 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -591,7 +825,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":757 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -600,7 +834,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -609,7 +843,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -618,7 +852,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":761 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -627,7 +861,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -635,6 +869,7 @@ typedef npy_double __pyx_t_5numpy_double_t; * ctypedef npy_cfloat cfloat_t */ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; +/* Declarations.proto */ #if CYTHON_CCOMPLEX #ifdef __cplusplus typedef ::std::complex< float > __pyx_t_float_complex; @@ -644,7 +879,9 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; #else typedef struct { float real, imag; } __pyx_t_float_complex; #endif +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); +/* Declarations.proto */ #if CYTHON_CCOMPLEX #ifdef __cplusplus typedef ::std::complex< double > __pyx_t_double_complex; @@ -654,14 +891,15 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; #else typedef struct { double real, imag; } __pyx_t_double_complex; #endif +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); /*--- Type declarations ---*/ -struct __pyx_obj_8specfile_SpecFile; -struct __pyx_obj_8specfile___pyx_scope_struct____iter__; -struct __pyx_obj_8specfile___pyx_scope_struct_1___iter__; +struct __pyx_obj_4silx_2io_8specfile_SpecFile; +struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct____iter__; +struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct_1___iter__; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":764 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -670,7 +908,7 @@ struct __pyx_obj_8specfile___pyx_scope_struct_1___iter__; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":765 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -679,7 +917,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":764 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":766 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -688,7 +926,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":768 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -704,31 +942,30 @@ typedef npy_cdouble __pyx_t_5numpy_complex_t; * * cdef extern from "SpecFileCython.h": */ -typedef struct _SpecFile __pyx_t_16specfile_wrapper_SpecFileHandle; +typedef struct _SpecFile __pyx_t_4silx_2io_16specfile_wrapper_SpecFileHandle; -/* "specfile.pyx":647 +/* "silx/io/specfile.pyx":644 * * * cdef class SpecFile(object): # <<<<<<<<<<<<<< * """ * */ -struct __pyx_obj_8specfile_SpecFile { +struct __pyx_obj_4silx_2io_8specfile_SpecFile { PyObject_HEAD - __pyx_t_16specfile_wrapper_SpecFileHandle *handle; + __pyx_t_4silx_2io_16specfile_wrapper_SpecFileHandle *handle; PyObject *filename; - int __pyx___open_failed; }; -/* "specfile.pyx":315 +/* "silx/io/specfile.pyx":314 * mca_index) * * def __iter__(self): # <<<<<<<<<<<<<< * """Return the next MCA data line each time this method is called. * */ -struct __pyx_obj_8specfile___pyx_scope_struct____iter__ { +struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct____iter__ { PyObject_HEAD Py_ssize_t __pyx_v_mca_index; PyObject *__pyx_v_self; @@ -737,21 +974,24 @@ struct __pyx_obj_8specfile___pyx_scope_struct____iter__ { }; -/* "specfile.pyx":698 +/* "silx/io/specfile.pyx":694 * return specfile_wrapper.SfScanNo(self.handle) * * def __iter__(self): # <<<<<<<<<<<<<< * """Return the next :class:`Scan` in a SpecFile each time this method * is called. */ -struct __pyx_obj_8specfile___pyx_scope_struct_1___iter__ { +struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct_1___iter__ { PyObject_HEAD Py_ssize_t __pyx_v_scan_index; - struct __pyx_obj_8specfile_SpecFile *__pyx_v_self; + struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self; Py_ssize_t __pyx_t_0; Py_ssize_t __pyx_t_1; }; + +/* --- Runtime support code (head) --- */ +/* Refnanny.proto */ #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif @@ -768,19 +1008,19 @@ struct __pyx_obj_8specfile___pyx_scope_struct_1___iter__ { static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; #ifdef WITH_THREAD - #define __Pyx_RefNannySetupContext(name, acquire_gil) \ - if (acquire_gil) { \ - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); 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\ - r = v; __Pyx_XDECREF(tmp); \ +#define __Pyx_XDECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_XDECREF(tmp);\ } while (0) -#define __Pyx_DECREF_SET(r, v) do { \ - PyObject *tmp = (PyObject *) r; \ - r = v; __Pyx_DECREF(tmp); \ +#define __Pyx_DECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_DECREF(tmp);\ } while (0) #define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) #define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) -#if CYTHON_COMPILING_IN_CPYTHON +/* PyObjectGetAttrStr.proto */ +#if CYTHON_USE_TYPE_SLOTS static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { PyTypeObject* tp = Py_TYPE(obj); if (likely(tp->tp_getattro)) @@ -829,18 +1070,23 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject #define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) #endif +/* GetBuiltinName.proto */ static PyObject *__Pyx_GetBuiltinName(PyObject *name); +/* RaiseArgTupleInvalid.proto */ static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); +/* RaiseDoubleKeywords.proto */ static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); -static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ - PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ +/* ParseKeywords.proto */ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ const char* function_name); -#if CYTHON_COMPILING_IN_CPYTHON +/* PyObjectSetAttrStr.proto */ +#if CYTHON_USE_TYPE_SLOTS #define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o,n,NULL) static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) { PyTypeObject* tp = Py_TYPE(obj); @@ -857,30 +1103,54 @@ static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr #define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v) #endif +/* PyCFunctionFastCall.proto */ +#if CYTHON_FAST_PYCCALL +static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs); +#else +#define __Pyx_PyCFunction_FastCall(func, args, nargs) (assert(0), NULL) +#endif + +/* PyFunctionFastCall.proto */ +#if CYTHON_FAST_PYCALL +#define __Pyx_PyFunction_FastCall(func, args, nargs)\ + __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) +#if 1 || PY_VERSION_HEX < 0x030600B1 +static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs); +#else +#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs) +#endif +#endif + +/* PyObjectCall.proto */ #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); #else #define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) #endif +/* PyObjectCallMethO.proto */ #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); #endif +/* PyObjectCallOneArg.proto */ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); +/* PyObjectCallNoArg.proto */ #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); #else #define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) #endif -static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) { +/* PySequenceContains.proto */ +static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) { int result = PySequence_Contains(seq, item); return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } -#if CYTHON_COMPILING_IN_CPYTHON +/* ListCompAppend.proto */ +#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { PyListObject* L = (PyListObject*) list; Py_ssize_t len = Py_SIZE(list); @@ -896,15 +1166,20 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { #define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) #endif +/* RaiseTooManyValuesToUnpack.proto */ static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); +/* RaiseNeedMoreValuesToUnpack.proto */ static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); +/* IterFinish.proto */ static CYTHON_INLINE int __Pyx_IterFinish(void); +/* UnpackItemEndCheck.proto */ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); -#if CYTHON_COMPILING_IN_CPYTHON +/* ListAppend.proto */ +#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { PyListObject* L = (PyListObject*) list; Py_ssize_t len = Py_SIZE(list); @@ -920,24 +1195,35 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { #define __Pyx_PyList_Append(L,x) PyList_Append(L,x) #endif +/* PyObjectCallMethod1.proto */ static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg); +/* append.proto */ static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x); -#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \ +/* PyIntBinop.proto */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace); +#else +#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace)\ + (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) +#endif + +/* GetItemInt.proto */ +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, int wraparound, int boundscheck); @@ -945,22 +1231,77 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, int wraparound, int boundscheck); -static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); -static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); +/* PyIntBinop.proto */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace); +#else +#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace)\ + (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2)) +#endif + +/* PyThreadStateGet.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate; +#define __Pyx_PyThreadState_assign __pyx_tstate = PyThreadState_GET(); +#else +#define __Pyx_PyThreadState_declare +#define __Pyx_PyThreadState_assign +#endif +/* PyErrFetchRestore.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb) +#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb) +#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb) +#define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else +#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb) +#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb) +#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb) +#endif + +/* RaiseException.proto */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); -static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); -static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); +/* SaveResetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); +#else +#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) +#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) +#endif + +/* PyErrExceptionMatches.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) +static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); +#else +#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) +#endif +/* GetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) +static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); +#endif +/* GetModuleGlobalName.proto */ static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); +/* WriteUnraisableException.proto */ static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename, - int full_traceback); + int full_traceback, int nogil); +/* StringJoin.proto */ #if PY_MAJOR_VERSION < 3 #define __Pyx_PyString_Join __Pyx_PyBytes_Join #define __Pyx_PyBaseString_Join(s, v) (PyUnicode_CheckExact(s) ? PyUnicode_Join(s, v) : __Pyx_PyBytes_Join(s, v)) @@ -978,12 +1319,14 @@ static void __Pyx_WriteUnraisable(const char *name, int clineno, static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values); #endif -static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) { +/* PyDictContains.proto */ +static CYTHON_INLINE int __Pyx_PyDict_ContainsTF(PyObject* item, PyObject* dict, int eq) { int result = PyDict_Contains(dict, item); return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } -#if PY_MAJOR_VERSION >= 3 +/* DictGetItem.proto */ +#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { PyObject *value; value = PyDict_GetItemWithError(d, key); @@ -1003,11 +1346,13 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) #endif +/* decode_c_bytes.proto */ static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes( const char* cstring, Py_ssize_t length, Py_ssize_t start, Py_ssize_t stop, const char* encoding, const char* errors, PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); +/* decode_bytes.proto */ static CYTHON_INLINE PyObject* __Pyx_decode_bytes( PyObject* string, Py_ssize_t start, Py_ssize_t stop, const char* encoding, const char* errors, @@ -1017,47 +1362,67 @@ static CYTHON_INLINE PyObject* __Pyx_decode_bytes( start, stop, encoding, errors, decode_func); } +/* PyIntBinop.proto */ +#if !CYTHON_COMPILING_IN_PYPY +static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, int inplace); +#else +#define __Pyx_PyInt_EqObjC(op1, op2, intval, inplace)\ + PyObject_RichCompare(op1, op2, Py_EQ) + #endif + +/* ExtTypeTest.proto */ static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); -#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) : \ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) : \ +/* SetItemInt.proto */ +#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) :\ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) :\ __Pyx_SetItemInt_Generic(o, to_py_func(i), v))) static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v); static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, int is_list, int wraparound, int boundscheck); +/* IncludeStringH.proto */ #include <string.h> +/* decode_c_string.proto */ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( const char* cstring, Py_ssize_t start, Py_ssize_t stop, const char* encoding, const char* errors, PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); +/* RaiseNoneIterError.proto */ static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); +/* Import.proto */ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +/* CalculateMetaclass.proto */ static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases); +/* Py3ClassCreate.proto */ static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc); static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, PyObject *dict, PyObject *mkw, int calculate_metaclass, int allow_py2_metaclass); +/* FetchCommonType.proto */ static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); +/* CythonFunction.proto */ #define __Pyx_CyFunction_USED 1 #include <structmember.h> #define __Pyx_CYFUNCTION_STATICMETHOD 0x01 #define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 #define __Pyx_CYFUNCTION_CCLASS 0x04 -#define __Pyx_CyFunction_GetClosure(f) \ +#define __Pyx_CyFunction_GetClosure(f)\ (((__pyx_CyFunctionObject *) (f))->func_closure) -#define __Pyx_CyFunction_GetClassObj(f) \ +#define __Pyx_CyFunction_GetClassObj(f)\ (((__pyx_CyFunctionObject *) (f))->func_classobj) -#define __Pyx_CyFunction_Defaults(type, f) \ +#define __Pyx_CyFunction_Defaults(type, f)\ ((type *)(((__pyx_CyFunctionObject *) (f))->defaults)) -#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \ +#define __Pyx_CyFunction_SetDefaultsGetter(f, g)\ ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g) typedef struct { PyCFunctionObject func; @@ -1081,7 +1446,7 @@ typedef struct { PyObject *func_annotations; } __pyx_CyFunctionObject; static PyTypeObject *__pyx_CyFunctionType = 0; -#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code) \ +#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code)\ __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, globals, code) static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml, int flags, PyObject* qualname, @@ -1097,11 +1462,12 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m, PyObject *dict); static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m, PyObject *dict); -static int __Pyx_CyFunction_init(void); +static int __pyx_CyFunction_init(void); +/* CodeObjectCache.proto */ typedef struct { - int code_line; PyCodeObject* code_object; + int code_line; } __Pyx_CodeObjectCacheEntry; struct __Pyx_CodeObjectCache { int count; @@ -1113,19 +1479,17 @@ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int co static PyCodeObject *__pyx_find_code_object(int code_line); static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); +/* AddTraceback.proto */ static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename); -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); - +/* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); - +/* CIntToPy.proto */ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); - +/* RealImag.proto */ #if CYTHON_CCOMPLEX #ifdef __cplusplus #define __Pyx_CREAL(z) ((z).real()) @@ -1138,7 +1502,8 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); #define __Pyx_CREAL(z) ((z).real) #define __Pyx_CIMAG(z) ((z).imag) #endif -#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX +#if defined(__cplusplus) && CYTHON_CCOMPLEX\ + && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103) #define __Pyx_SET_CREAL(z,x) ((z).real(x)) #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) #else @@ -1146,93 +1511,104 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) #endif -static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); - +/* Arithmetic.proto */ #if CYTHON_CCOMPLEX - #define __Pyx_c_eqf(a, b) ((a)==(b)) - #define __Pyx_c_sumf(a, b) ((a)+(b)) - #define __Pyx_c_difff(a, b) ((a)-(b)) - #define __Pyx_c_prodf(a, b) ((a)*(b)) - #define __Pyx_c_quotf(a, b) ((a)/(b)) - #define __Pyx_c_negf(a) (-(a)) + #define __Pyx_c_eq_float(a, b) ((a)==(b)) + #define __Pyx_c_sum_float(a, b) ((a)+(b)) + #define __Pyx_c_diff_float(a, b) ((a)-(b)) + #define __Pyx_c_prod_float(a, b) ((a)*(b)) + #define __Pyx_c_quot_float(a, b) ((a)/(b)) + #define __Pyx_c_neg_float(a) (-(a)) #ifdef __cplusplus - #define __Pyx_c_is_zerof(z) ((z)==(float)0) - #define __Pyx_c_conjf(z) (::std::conj(z)) + #define __Pyx_c_is_zero_float(z) ((z)==(float)0) + #define __Pyx_c_conj_float(z) (::std::conj(z)) #if 1 - #define __Pyx_c_absf(z) (::std::abs(z)) - #define __Pyx_c_powf(a, b) (::std::pow(a, b)) + #define __Pyx_c_abs_float(z) (::std::abs(z)) + #define __Pyx_c_pow_float(a, b) (::std::pow(a, b)) #endif #else - #define __Pyx_c_is_zerof(z) ((z)==0) - #define __Pyx_c_conjf(z) (conjf(z)) + #define __Pyx_c_is_zero_float(z) ((z)==0) + #define __Pyx_c_conj_float(z) (conjf(z)) #if 1 - #define __Pyx_c_absf(z) (cabsf(z)) - #define __Pyx_c_powf(a, b) (cpowf(a, b)) + #define __Pyx_c_abs_float(z) (cabsf(z)) + #define __Pyx_c_pow_float(a, b) (cpowf(a, b)) #endif #endif #else - static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); - static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex); #if 1 - static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex); #endif #endif -static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); - +/* Arithmetic.proto */ #if CYTHON_CCOMPLEX - #define __Pyx_c_eq(a, b) ((a)==(b)) - #define __Pyx_c_sum(a, b) ((a)+(b)) - #define __Pyx_c_diff(a, b) ((a)-(b)) - #define __Pyx_c_prod(a, b) ((a)*(b)) - #define __Pyx_c_quot(a, b) ((a)/(b)) - #define __Pyx_c_neg(a) (-(a)) + #define __Pyx_c_eq_double(a, b) ((a)==(b)) + #define __Pyx_c_sum_double(a, b) ((a)+(b)) + #define __Pyx_c_diff_double(a, b) ((a)-(b)) + #define __Pyx_c_prod_double(a, b) ((a)*(b)) + #define __Pyx_c_quot_double(a, b) ((a)/(b)) + #define __Pyx_c_neg_double(a) (-(a)) #ifdef __cplusplus - #define __Pyx_c_is_zero(z) ((z)==(double)0) - #define __Pyx_c_conj(z) (::std::conj(z)) + #define __Pyx_c_is_zero_double(z) ((z)==(double)0) + #define __Pyx_c_conj_double(z) (::std::conj(z)) #if 1 - #define __Pyx_c_abs(z) (::std::abs(z)) - #define __Pyx_c_pow(a, b) (::std::pow(a, b)) + #define __Pyx_c_abs_double(z) (::std::abs(z)) + #define __Pyx_c_pow_double(a, b) (::std::pow(a, b)) #endif #else - #define __Pyx_c_is_zero(z) ((z)==0) - #define __Pyx_c_conj(z) (conj(z)) + #define __Pyx_c_is_zero_double(z) ((z)==0) + #define __Pyx_c_conj_double(z) (conj(z)) #if 1 - #define __Pyx_c_abs(z) (cabs(z)) - #define __Pyx_c_pow(a, b) (cpow(a, b)) + #define __Pyx_c_abs_double(z) (cabs(z)) + #define __Pyx_c_pow_double(a, b) (cpow(a, b)) #endif #endif #else - static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); - static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex); #if 1 - static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex); #endif #endif +/* CIntToPy.proto */ +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); + +/* CIntFromPy.proto */ +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +/* CIntFromPy.proto */ +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +/* SwapException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); +#endif -#define __Pyx_Generator_USED -#include <structmember.h> -#include <frameobject.h> -typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *); +/* CoroutineBase.proto */ +typedef PyObject *(*__pyx_coroutine_body_t)(PyObject *, PyObject *); typedef struct { PyObject_HEAD - __pyx_generator_body_t body; + __pyx_coroutine_body_t body; PyObject *closure; PyObject *exc_type; PyObject *exc_value; @@ -1242,21 +1618,39 @@ typedef struct { PyObject *yieldfrom; PyObject *gi_name; PyObject *gi_qualname; + PyObject *gi_modulename; int resume_label; char is_running; -} __pyx_GeneratorObject; -static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, - PyObject *closure, PyObject *name, PyObject *qualname); -static int __pyx_Generator_init(void); -static int __Pyx_Generator_clear(PyObject* self); +} __pyx_CoroutineObject; +static __pyx_CoroutineObject *__Pyx__Coroutine_New( + PyTypeObject *type, __pyx_coroutine_body_t body, PyObject *closure, + PyObject *name, PyObject *qualname, PyObject *module_name); +static int __Pyx_Coroutine_clear(PyObject *self); #if 1 || PY_VERSION_HEX < 0x030300B0 static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue); #else #define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue) #endif +/* PatchModuleWithCoroutine.proto */ +static PyObject* __Pyx_Coroutine_patch_module(PyObject* module, const char* py_code); + +/* PatchGeneratorABC.proto */ +static int __Pyx_patch_abc(void); + +/* Generator.proto */ +#define __Pyx_Generator_USED +static PyTypeObject *__pyx_GeneratorType = 0; +#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType) +#define __Pyx_Generator_New(body, closure, name, qualname, module_name)\ + __Pyx__Coroutine_New(__pyx_GeneratorType, body, closure, name, qualname, module_name) +static PyObject *__Pyx_Generator_Next(PyObject *self); +static int __pyx_Generator_init(void); + +/* CheckBinaryVersion.proto */ static int __Pyx_check_binary_version(void); +/* PyIdentifierFromString.proto */ #if !defined(__Pyx_PyIdentifier_FromString) #if PY_MAJOR_VERSION < 3 #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) @@ -1265,28 +1659,33 @@ static int __Pyx_check_binary_version(void); #endif #endif +/* ModuleImport.proto */ static PyObject *__Pyx_ImportModule(const char *name); +/* TypeImport.proto */ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); +/* InitStrings.proto */ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /* Module declarations from 'cpython.buffer' */ -/* Module declarations from 'cpython.ref' */ - /* Module declarations from 'libc.string' */ /* Module declarations from 'libc.stdio' */ -/* Module declarations from 'cpython.object' */ - /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.type' */ static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; +/* Module declarations from 'cpython' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from 'cpython.ref' */ + /* Module declarations from 'libc.stdlib' */ /* Module declarations from 'numpy' */ @@ -1298,357 +1697,287 @@ static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ +static CYTHON_INLINE int __pyx_f_5numpy_import_array(void); /*proto*/ /* Module declarations from 'cython' */ -/* Module declarations from 'specfile_wrapper' */ +/* Module declarations from 'silx.io.specfile_wrapper' */ -/* Module declarations from 'specfile' */ -static PyTypeObject *__pyx_ptype_8specfile_SpecFile = 0; -static PyTypeObject *__pyx_ptype_8specfile___pyx_scope_struct____iter__ = 0; -static PyTypeObject *__pyx_ptype_8specfile___pyx_scope_struct_1___iter__ = 0; -#define __Pyx_MODULE_NAME "specfile" -int __pyx_module_is_main_specfile = 0; +/* Module declarations from 'silx.io.specfile' */ +static PyTypeObject *__pyx_ptype_4silx_2io_8specfile_SpecFile = 0; +static PyTypeObject *__pyx_ptype_4silx_2io_8specfile___pyx_scope_struct____iter__ = 0; +static PyTypeObject *__pyx_ptype_4silx_2io_8specfile___pyx_scope_struct_1___iter__ = 0; +#define __Pyx_MODULE_NAME "silx.io.specfile" +int __pyx_module_is_main_silx__io__specfile = 0; -/* Implementation of 'specfile' */ -static PyObject *__pyx_builtin_Exception; +/* Implementation of 'silx.io.specfile' */ +static PyObject *__pyx_builtin_MemoryError; +static PyObject *__pyx_builtin_IOError; +static PyObject *__pyx_builtin_KeyError; +static PyObject *__pyx_builtin_IndexError; static PyObject *__pyx_builtin_object; static PyObject *__pyx_builtin_property; static PyObject *__pyx_builtin_map; static PyObject *__pyx_builtin_range; -static PyObject *__pyx_builtin_IndexError; static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_open; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_ValueError; -static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_AttributeError; static PyObject *__pyx_builtin_RuntimeError; -static PyObject *__pyx_pf_8specfile_3MCA___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_scan); /* proto */ -static PyObject *__pyx_pf_8specfile_3MCA_2_parse_channels(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_3MCA_4_parse_calibration(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_3MCA_6__len__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_3MCA_8__getitem__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ -static PyObject *__pyx_pf_8specfile_3MCA_10__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile__add_or_concatenate(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_dictionary, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_specfile, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_2index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_4number(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_6order(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_8header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_10scan_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_12file_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_14scan_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_16mca_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_18file_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_20labels(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_22data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_24mca(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_26motor_names(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_28motor_positions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_30record_exists_in_hdr(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_record); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_32data_line(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line_index); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_34data_column_by_name(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_label); /* proto */ -static PyObject *__pyx_pf_8specfile_4Scan_36motor_position_by_name(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_pf_8specfile_2_string_to_char_star(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string_); /* proto */ -static PyObject *__pyx_pf_8specfile_4is_specfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename); /* proto */ -static int __pyx_pf_8specfile_8SpecFile___cinit__(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ -static int __pyx_pf_8specfile_8SpecFile_2__init__(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ -static void __pyx_pf_8specfile_8SpecFile_4__dealloc__(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_pf_8specfile_8SpecFile_6__len__(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_8__iter__(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_11__getitem__(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_13keys(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self); /* proto */ -static int __pyx_pf_8specfile_8SpecFile_15__contains__(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_17_get_error_string(CYTHON_UNUSED struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_error_code); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_19_handle_error(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_error_code); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_21index(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_number, PyObject *__pyx_v_scan_order); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_23number(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_25order(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_27_list(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_29list(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_31data(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_33data_column_by_name(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_label); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_35scan_header(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_37file_header(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_39columns(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_41command(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_43date(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_45labels(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_47motor_names(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_49motor_positions(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_51motor_position_by_name(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_53number_of_mca(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_55mca_calibration(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_8specfile_8SpecFile_57get_mca(struct __pyx_obj_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_mca_index); /* proto */ -static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ -static PyObject *__pyx_tp_new_8specfile_SpecFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_8specfile___pyx_scope_struct____iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_8specfile___pyx_scope_struct_1___iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static char __pyx_k_[] = "\n"; -static char __pyx_k_2[] = " {2,}"; -static char __pyx_k_3[] = "3"; -static char __pyx_k_B[] = "B"; -static char __pyx_k_F[] = "#F "; -static char __pyx_k_H[] = "H"; -static char __pyx_k_I[] = "I"; -static char __pyx_k_L[] = "L"; -static char __pyx_k_O[] = "O"; -static char __pyx_k_Q[] = "Q"; -static char __pyx_k_S[] = "#S "; -static char __pyx_k_b[] = "b"; -static char __pyx_k_d[] = "d"; -static char __pyx_k_f[] = "f"; -static char __pyx_k_g[] = "g"; -static char __pyx_k_h[] = "h"; -static char __pyx_k_i[] = "i"; -static char __pyx_k_l[] = "l"; -static char __pyx_k_q[] = "q"; -static char __pyx_k_w[] = "#(\\w+) *(.*)"; -static char __pyx_k_Zd[] = "Zd"; -static char __pyx_k_Zf[] = "Zf"; -static char __pyx_k_Zg[] = "Zg"; -static char __pyx_k__7[] = "#"; -static char __pyx_k_os[] = "os"; -static char __pyx_k_re[] = "re"; -static char __pyx_k_MCA[] = "MCA"; -static char __pyx_k_MIT[] = "MIT"; -static char __pyx_k__14[] = " "; -static char __pyx_k__25[] = "."; -static char __pyx_k__27[] = "', '"; -static char __pyx_k__28[] = "'"; -static char __pyx_k__29[] = ""; -static char __pyx_k_d_d[] = "%d.%d"; -static char __pyx_k_doc[] = "__doc__"; -static char __pyx_k_key[] = "key"; -static char __pyx_k_len[] = "__len__"; -static char __pyx_k_map[] = "map"; -static char __pyx_k_mca[] = "_mca"; -static char __pyx_k_msg[] = "msg"; -static char __pyx_k_ret[] = "ret"; -static char __pyx_k_sub[] = "sub"; -static char __pyx_k_sys[] = "sys"; -static char __pyx_k_w_2[] = "#@(\\w+) *(.*)"; -static char __pyx_k_Scan[] = "Scan"; -static char __pyx_k_args[] = "args"; -static char __pyx_k_data[] = "_data"; -static char __pyx_k_date[] = "__date__"; -static char __pyx_k_hkey[] = "hkey"; -static char __pyx_k_init[] = "__init__"; -static char __pyx_k_iter[] = "__iter__"; -static char __pyx_k_join[] = "join"; -static char __pyx_k_keys[] = "keys"; -static char __pyx_k_line[] = "line"; -static char __pyx_k_list[] = "_list"; -static char __pyx_k_main[] = "__main__"; -static char __pyx_k_name[] = "name"; -static char __pyx_k_open[] = "open"; -static char __pyx_k_path[] = "path"; -static char __pyx_k_scan[] = "scan"; -static char __pyx_k_self[] = "self"; -static char __pyx_k_send[] = "send"; -static char __pyx_k_stop[] = "stop"; -static char __pyx_k_test[] = "__test__"; -static char __pyx_k_CALIB[] = "CALIB"; -static char __pyx_k_CHANN[] = "CHANN"; -static char __pyx_k_ascii[] = "ascii"; -static char __pyx_k_close[] = "close"; -static char __pyx_k_dtype[] = "dtype"; -static char __pyx_k_empty[] = "empty"; -static char __pyx_k_group[] = "group"; -static char __pyx_k_index[] = "index"; -static char __pyx_k_label[] = "label"; -static char __pyx_k_match[] = "match"; -static char __pyx_k_mca_2[] = "mca"; -static char __pyx_k_numpy[] = "numpy"; -static char __pyx_k_order[] = "order"; -static char __pyx_k_range[] = "range"; -static char __pyx_k_shape[] = "shape"; -static char __pyx_k_split[] = "split"; -static char __pyx_k_start[] = "start"; -static char __pyx_k_strip[] = "strip"; -static char __pyx_k_throw[] = "throw"; -static char __pyx_k_value[] = "value"; -static char __pyx_k_ERRORS[] = "ERRORS"; -static char __pyx_k_append[] = "append"; -static char __pyx_k_data_2[] = "data"; -static char __pyx_k_decode[] = "decode"; -static char __pyx_k_double[] = "double"; -static char __pyx_k_encode[] = "encode"; -static char __pyx_k_header[] = "_header"; -static char __pyx_k_hvalue[] = "hvalue"; -static char __pyx_k_import[] = "__import__"; -static char __pyx_k_isfile[] = "isfile"; -static char __pyx_k_labels[] = "_labels"; -static char __pyx_k_length[] = "length"; -static char __pyx_k_logger[] = "_logger"; -static char __pyx_k_lstrip[] = "lstrip"; -static char __pyx_k_module[] = "__module__"; -static char __pyx_k_name_2[] = "__name__"; -static char __pyx_k_number[] = "number"; -static char __pyx_k_object[] = "object"; -static char __pyx_k_record[] = "record"; -static char __pyx_k_scan_2[] = "_scan"; -static char __pyx_k_search[] = "search"; -static char __pyx_k_string[] = "string_"; -static char __pyx_k_SfError[] = "SfError"; -static char __pyx_k_authors[] = "__authors__"; -static char __pyx_k_get_mca[] = "get_mca"; -static char __pyx_k_getitem[] = "__getitem__"; -static char __pyx_k_index_2[] = "_index"; -static char __pyx_k_license[] = "__license__"; -static char __pyx_k_logging[] = "logging"; -static char __pyx_k_order_2[] = "_order"; -static char __pyx_k_os_path[] = "os.path"; -static char __pyx_k_prepare[] = "__prepare__"; -static char __pyx_k_version[] = "version"; -static char __pyx_k_warning[] = "warning"; -static char __pyx_k_KeyError[] = "KeyError"; -static char __pyx_k_L_header[] = "L_header"; -static char __pyx_k_P_Knobel[] = "P. Knobel"; -static char __pyx_k_Scan_mca[] = "Scan.mca"; -static char __pyx_k_channels[] = "channels"; -static char __pyx_k_filename[] = "filename"; -static char __pyx_k_header_2[] = "header"; -static char __pyx_k_labels_2[] = "labels"; -static char __pyx_k_number_2[] = "_number"; -static char __pyx_k_property[] = "property"; -static char __pyx_k_qualname[] = "__qualname__"; -static char __pyx_k_specfile[] = "_specfile"; -static char __pyx_k_Exception[] = "Exception"; -static char __pyx_k_MCA___len[] = "MCA.__len__"; -static char __pyx_k_Scan_data[] = "Scan.data"; -static char __pyx_k_TypeError[] = "TypeError"; -static char __pyx_k_data_line[] = "data_line"; -static char __pyx_k_enumerate[] = "enumerate"; -static char __pyx_k_getLogger[] = "getLogger"; -static char __pyx_k_increment[] = "increment"; -static char __pyx_k_match_mca[] = "match_mca"; -static char __pyx_k_mca_index[] = "mca_index"; -static char __pyx_k_metaclass[] = "__metaclass__"; -static char __pyx_k_transpose[] = "transpose"; -static char __pyx_k_27_09_2016[] = "27/09/2016"; -static char __pyx_k_IndexError[] = "IndexError"; -static char __pyx_k_MCA___init[] = "MCA.__init__"; -static char __pyx_k_MCA___iter[] = "MCA.__iter__"; -static char __pyx_k_Scan_index[] = "Scan.index"; -static char __pyx_k_Scan_order[] = "Scan.order"; -static char __pyx_k_Valid_keys[] = "\nValid keys: '"; -static char __pyx_k_ValueError[] = "ValueError"; -static char __pyx_k_calib_line[] = "calib_line"; -static char __pyx_k_chann_line[] = "chann_line"; -static char __pyx_k_dictionary[] = "dictionary"; -static char __pyx_k_line_index[] = "line_index"; -static char __pyx_k_scan_index[] = "scan_index"; -static char __pyx_k_scan_order[] = "scan_order"; -static char __pyx_k_specfile_2[] = "specfile"; -static char __pyx_k_startswith[] = "startswith"; -static char __pyx_k_Scan___init[] = "Scan.__init__"; -static char __pyx_k_Scan_header[] = "Scan.header"; -static char __pyx_k_Scan_labels[] = "Scan.labels"; -static char __pyx_k_Scan_number[] = "Scan.number"; -static char __pyx_k_basicConfig[] = "basicConfig"; -static char __pyx_k_calib_lines[] = "calib_lines"; -static char __pyx_k_calibration[] = "calibration"; -static char __pyx_k_chann_lines[] = "chann_lines"; -static char __pyx_k_file_header[] = "file_header"; -static char __pyx_k_is_specfile[] = "is_specfile"; -static char __pyx_k_motor_names[] = "motor_names"; -static char __pyx_k_scan_header[] = "scan_header"; -static char __pyx_k_scan_number[] = "scan_number"; -static char __pyx_k_RuntimeError[] = "RuntimeError"; -static char __pyx_k_SfNoMcaError[] = "SfNoMcaError"; -static char __pyx_k_handle_error[] = "_handle_error"; -static char __pyx_k_version_info[] = "version_info"; -static char __pyx_k_MCA___getitem[] = "MCA.__getitem__"; -static char __pyx_k_SfErrFileOpen[] = "SfErrFileOpen"; -static char __pyx_k_SfErrFileRead[] = "SfErrFileRead"; -static char __pyx_k_motor_names_2[] = "_motor_names"; -static char __pyx_k_number_of_mca[] = "number_of_mca"; -static char __pyx_k_AttributeError[] = "AttributeError"; -static char __pyx_k_Scan_data_line[] = "Scan.data_line"; -static char __pyx_k_SfErrFileClose[] = "SfErrFileClose"; -static char __pyx_k_SfErrFileWrite[] = "SfErrFileWrite"; -static char __pyx_k_SfErrLineEmpty[] = "SfErrLineEmpty"; -static char __pyx_k_parse_channels[] = "_parse_channels"; -static char __pyx_k_SpecFile___iter[] = "SpecFile.__iter__"; -static char __pyx_k_mca_header_dict[] = "mca_header_dict"; -static char __pyx_k_motor_positions[] = "motor_positions"; -static char __pyx_k_SF_ERR_FILE_OPEN[] = "SF_ERR_FILE_OPEN"; -static char __pyx_k_SF_ERR_NO_ERRORS[] = "SF_ERR_NO_ERRORS"; -static char __pyx_k_Scan_file_header[] = "Scan.file_header"; -static char __pyx_k_Scan_motor_names[] = "Scan.motor_names"; -static char __pyx_k_Scan_scan_header[] = "Scan.scan_header"; -static char __pyx_k_SfErrColNotFound[] = "SfErrColNotFound"; -static char __pyx_k_SfErrMcaNotFound[] = "SfErrMcaNotFound"; -static char __pyx_k_SfErrMemoryAlloc[] = "SfErrMemoryAlloc"; -static char __pyx_k_all_calib_values[] = "all_calib_values"; -static char __pyx_k_all_chann_values[] = "all_chann_values"; -static char __pyx_k_file_header_dict[] = "_file_header_dict"; -static char __pyx_k_get_error_string[] = "_get_error_string"; -static char __pyx_k_scan_header_dict[] = "_scan_header_dict"; -static char __pyx_k_SfErrLineNotFound[] = "SfErrLineNotFound"; -static char __pyx_k_SfErrScanNotFound[] = "SfErrScanNotFound"; -static char __pyx_k_SfErrUserNotFound[] = "SfErrUserNotFound"; -static char __pyx_k_file_header_lines[] = "_file_header_lines"; -static char __pyx_k_mca_header_dict_2[] = "_mca_header_dict"; -static char __pyx_k_motor_positions_2[] = "_motor_positions"; -static char __pyx_k_parse_calibration[] = "_parse_calibration"; -static char __pyx_k_scan_header_lines[] = "_scan_header_lines"; -static char __pyx_k_SfErrLabelNotFound[] = "SfErrLabelNotFound"; -static char __pyx_k_SfErrMotorNotFound[] = "SfErrMotorNotFound"; -static char __pyx_k_SfNoMca_returned_1[] = "(SfNoMca returned -1)"; -static char __pyx_k_add_or_concatenate[] = "_add_or_concatenate"; -static char __pyx_k_file_header_dict_2[] = "file_header_dict"; -static char __pyx_k_scan_header_dict_2[] = "scan_header_dict"; -static char __pyx_k_MCA__parse_channels[] = "MCA._parse_channels"; -static char __pyx_k_SfErrHeaderNotFound[] = "SfErrHeaderNotFound"; -static char __pyx_k_data_column_by_name[] = "data_column_by_name"; -static char __pyx_k_string_to_char_star[] = "_string_to_char_star"; -static char __pyx_k_Scan_mca_header_dict[] = "Scan.mca_header_dict"; -static char __pyx_k_Scan_motor_positions[] = "Scan.motor_positions"; -static char __pyx_k_record_exists_in_hdr[] = "record_exists_in_hdr"; -static char __pyx_k_SF_ERR_SCAN_NOT_FOUND[] = "SF_ERR_SCAN_NOT_FOUND"; -static char __pyx_k_Scan_file_header_dict[] = "Scan.file_header_dict"; -static char __pyx_k_Scan_scan_header_dict[] = "Scan.scan_header_dict"; -static char __pyx_k_SfErrPositionNotFound[] = "SfErrPositionNotFound"; -static char __pyx_k_one_line_calib_values[] = "one_line_calib_values"; -static char __pyx_k_one_line_chann_values[] = "one_line_chann_values"; -static char __pyx_k_MCA__parse_calibration[] = "MCA._parse_calibration"; -static char __pyx_k_motor_position_by_name[] = "motor_position_by_name"; -static char __pyx_k_Scan_data_column_by_name[] = "Scan.data_column_by_name"; -static char __pyx_k_Scan_record_exists_in_hdr[] = "Scan.record_exists_in_hdr"; -static char __pyx_k_Scan_motor_position_by_name[] = "Scan.motor_position_by_name"; -static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; -static char __pyx_k_Error_while_closing_SpecFile[] = "Error while closing SpecFile"; -static char __pyx_k_number_and_M_the_order_eg_2_3[] = " number and M the order (eg '2.3')."; -static char __pyx_k_MCA_index_must_be_in_range_0_d[] = "MCA index must be in range 0-%d"; -static char __pyx_k_param_specfile_Parent_SpecFile[] = "\n\n :param specfile: Parent SpecFile from which this scan is extracted.\n :type specfile: :class:`SpecFile`\n :param scan_index: Unique index defining the scan in the SpecFile\n :type scan_index: int\n\n Interface to access a SpecFile scan\n\n A scan is a block of descriptive header lines followed by a 2D data array.\n\n Following three ways of accessing a scan are equivalent::\n\n sf = SpecFile(\"/path/to/specfile.dat\")\n\n # Explicit class instantiation\n scan2 = Scan(sf, scan_index=2)\n\n # 0-based index on a SpecFile object\n scan2 = sf[2]\n\n # Using a \"n.m\" key (scan number starting with 1, scan order)\n scan2 = sf[\"3.1\"]\n "; -static char __pyx_k_users_payno_Documents_dev_esrf[] = "/users/payno/Documents/dev/esrf/silx/paynoSilx/silx/silx/io/specfile/specfile.pyx"; -static char __pyx_k_Base_exception_inherited_by_all[] = "Base exception inherited by all exceptions raised when a\n C function from the legacy SpecFile library returns an error\n code.\n "; -static char __pyx_k_Scan_index_must_be_in_range_0_d[] = "Scan index must be in range 0-%d"; -static char __pyx_k_The_scan_identification_key_can[] = "The scan identification key can be an integer representing "; -static char __pyx_k_This_module_is_a_cython_binding[] = "\nThis module is a cython binding to wrap the C SpecFile library, to access\nSpecFile data within a python program.\n\nDocumentation for the original C library SpecFile can be found on the ESRF\nwebsite:\n`The manual for the SpecFile Library <http://www.esrf.eu/files/live/sites/www/files/Instrumentation/software/beamline-control/BLISS/documentation/SpecFileManual.pdf>`_\n\nExamples\n========\n\nStart by importing :class:`SpecFile` and instantiate it:\n\n.. code-block:: python\n\n from silx.io.specfile import SpecFile\n\n sf = SpecFile(\"test.dat\")\n\nA :class:`SpecFile` instance can be accessed like a dictionary to obtain a\n:class:`Scan` instance.\n\nIf the key is a string representing two values\nseparated by a dot (e.g. ``\"1.2\"``), they will be treated as the scan number\n(``#S`` header line) and the scan order::\n\n # get second occurrence of scan \"#S 1\"\n myscan = sf[\"1.2\"]\n\n # access scan data as a numpy array\n nlines, ncolumns = myscan.data.shape\n\nIf the key is an integer, it will be treated as a 0-based index::\n\n first_scan = sf[0]\n second_scan = sf[1]\n\nIt is also possible to browse through all scans using :class:`SpecFile` as\nan iterator::\n\n for scan in sf:\n print(scan.scan_header_dict['S'])\n\nMCA spectra can be selectively loaded using an instance of :class:`MCA`\nprovided by :class:`Scan`::\n\n # Only one MCA spectrum is loaded in memory\n second_mca = first_scan.mca[1]\n\n # Iterating trough all MCA spectra in a scan:\n for mca_data in first_scan.mca:\n print(sum(mca_data))\n\nClasses\n=======\n\n- :class:`SpecFile`\n- :class:`Scan`\n- :class:`MCA`\n\nExceptions\n==========\n\n- :class:`SfError`\n- :class:`SfErrMemoryAlloc`\n- :class:`SfErrFileOpen`\n- :class:`SfErrFileClose`\n- :class:`SfErrFileRead`\n- :class:`SfErrFileWrite`\n- :class:`SfErrLineNotFound`\n- :class:`SfErrScanNotFound`\n- :class:`SfErrHeaderNotFound`\n- :class:`SfErrLabelNotFound`\n- :class:`SfErrMotorNotFound`""\n- :class:`SfErrPositionNotFound`\n- :class:`SfErrLineEmpty`\n- :class:`SfErrUserNotFound`\n- :class:`SfErrColNotFound`\n- :class:`SfErrMcaNotFound`\n\n"; -static char __pyx_k_param_scan_Parent_Scan_instance[] = "\n\n :param scan: Parent Scan instance\n :type scan: :class:`Scan`\n\n :var calibration: MCA calibration :math:`(a, b, c)` (as in\n :math:`a + b x + c x\302\262`) from ``#@CALIB`` scan header.\n :type calibration: list of 3 floats, default ``[0., 1., 0.]``\n :var channels: MCA channels list from ``#@CHANN`` scan header.\n In the absence of a ``#@CHANN`` header, this attribute is a list\n ``[0, \342\200\246, N-1]`` where ``N`` is the length of the first spectrum.\n In the absence of MCA spectra, this attribute defaults to ``None``.\n :type channels: list of int\n\n This class provides access to Multi-Channel Analysis data. A :class:`MCA`\n instance can be indexed to access 1D numpy arrays representing single \n MCA\302\240spectra.\n\n To create a :class:`MCA` instance, you must provide a parent :class:`Scan`\n instance, which in turn will provide a reference to the original\n :class:`SpecFile` instance::\n\n sf = SpecFile(\"/path/to/specfile.dat\")\n scan2 = Scan(sf, scan_index=2)\n mcas_in_scan2 = MCA(scan2)\n for i in len(mcas_in_scan2):\n mca_data = mcas_in_scan2[i]\n ... # do some something with mca_data (1D numpy array)\n\n A more pythonic way to do the same work, without having to explicitly\n instantiate ``scan`` and ``mcas_in_scan``, would be::\n\n sf = SpecFile(\"specfilename.dat\")\n # scan2 from previous example can be referred to as sf[2]\n # mcas_in_scan2 from previous example can be referred to as scan2.mca\n for mca_data in sf[2].mca:\n ... # do some something with mca_data (1D numpy array)\n\n "; -static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; -static char __pyx_k_Cannot_get_data_column_s_in_scan[] = "Cannot get data column %s in scan %d.%d"; -static char __pyx_k_Custom_exception_raised_when_SfN[] = "Custom exception raised when ``SfNoMca()`` returns ``-1``\n "; -static char __pyx_k_Failed_to_retrieve_number_of_MCA[] = "Failed to retrieve number of MCA "; -static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; -static char __pyx_k_MCA_calibration_line_CALIB_not_f[] = "MCA calibration line (@CALIB) not found"; -static char __pyx_k_MCA_index_should_be_an_integer_s[] = "MCA index should be an integer (%s provided)"; -static char __pyx_k_No_MCA_spectrum_found_in_this_sc[] = "No MCA spectrum found in this scan"; -static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; -static char __pyx_k_Parameter_value_must_be_a_string[] = "Parameter value must be a string."; -static char __pyx_k_Unable_to_parse_file_header_line[] = "Unable to parse file header line "; -static char __pyx_k_Unable_to_parse_scan_header_line[] = "Unable to parse scan header line "; -static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; -static char __pyx_k_the_unique_scan_index_or_a_strin[] = "the unique scan index or a string 'N.M' with N being the scan"; -static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_builtin_ImportError; +static const char __pyx_k_[] = "\n"; +static const char __pyx_k_2[] = " {2,}"; +static const char __pyx_k_3[] = "3"; +static const char __pyx_k_F[] = "#F "; +static const char __pyx_k_L[] = "L"; +static const char __pyx_k_S[] = "#S "; +static const char __pyx_k_f[] = "f"; +static const char __pyx_k_i[] = "i"; +static const char __pyx_k_w[] = "#(\\w+) *(.*)"; +static const char __pyx_k__7[] = "#"; +static const char __pyx_k_os[] = "os"; +static const char __pyx_k_re[] = "re"; +static const char __pyx_k_MCA[] = "MCA"; +static const char __pyx_k_MIT[] = "MIT"; +static const char __pyx_k__14[] = " "; +static const char __pyx_k__25[] = "."; +static const char __pyx_k__27[] = "', '"; +static const char __pyx_k__28[] = "'"; +static const char __pyx_k_d_d[] = "%d.%d"; +static const char __pyx_k_doc[] = "__doc__"; +static const char __pyx_k_key[] = "key"; +static const char __pyx_k_len[] = "__len__"; +static const char __pyx_k_map[] = "map"; +static const char __pyx_k_mca[] = "_mca"; +static const char __pyx_k_msg[] = "msg"; +static const char __pyx_k_ret[] = "ret"; +static const char __pyx_k_sub[] = "sub"; +static const char __pyx_k_sys[] = "sys"; +static const char __pyx_k_w_2[] = "#@(\\w+) *(.*)"; +static const char __pyx_k_Scan[] = "Scan"; +static const char __pyx_k_args[] = "args"; +static const char __pyx_k_data[] = "_data"; +static const char __pyx_k_date[] = "__date__"; +static const char __pyx_k_hkey[] = "hkey"; +static const char __pyx_k_init[] = "__init__"; +static const char __pyx_k_iter[] = "__iter__"; +static const char __pyx_k_join[] = "join"; +static const char __pyx_k_keys[] = "keys"; +static const char __pyx_k_line[] = "line"; +static const char __pyx_k_list[] = "_list"; +static const char __pyx_k_main[] = "__main__"; +static const char __pyx_k_name[] = "name"; +static const char __pyx_k_open[] = "open"; +static const char __pyx_k_path[] = "path"; +static const char __pyx_k_scan[] = "scan"; +static const char __pyx_k_self[] = "self"; +static const char __pyx_k_send[] = "send"; +static const char __pyx_k_stop[] = "stop"; +static const char __pyx_k_test[] = "__test__"; +static const char __pyx_k_CALIB[] = "CALIB"; +static const char __pyx_k_CHANN[] = "CHANN"; +static const char __pyx_k_ascii[] = "ascii"; +static const char __pyx_k_close[] = "close"; +static const char __pyx_k_dtype[] = "dtype"; +static const char __pyx_k_empty[] = "empty"; +static const char __pyx_k_group[] = "group"; +static const char __pyx_k_index[] = "index"; +static const char __pyx_k_label[] = "label"; +static const char __pyx_k_match[] = "match"; +static const char __pyx_k_mca_2[] = "mca"; +static const char __pyx_k_numpy[] = "numpy"; +static const char __pyx_k_order[] = "order"; +static const char __pyx_k_range[] = "range"; +static const char __pyx_k_shape[] = "shape"; +static const char __pyx_k_split[] = "split"; +static const char __pyx_k_start[] = "start"; +static const char __pyx_k_strip[] = "strip"; +static const char __pyx_k_throw[] = "throw"; +static const char __pyx_k_value[] = "value"; +static const char __pyx_k_ERRORS[] = "ERRORS"; +static const char __pyx_k_append[] = "append"; +static const char __pyx_k_data_2[] = "data"; +static const char __pyx_k_decode[] = "decode"; +static const char __pyx_k_double[] = "double"; +static const char __pyx_k_encode[] = "encode"; +static const char __pyx_k_header[] = "_header"; +static const char __pyx_k_hvalue[] = "hvalue"; +static const char __pyx_k_import[] = "__import__"; +static const char __pyx_k_isfile[] = "isfile"; +static const char __pyx_k_labels[] = "_labels"; +static const char __pyx_k_length[] = "length"; +static const char __pyx_k_logger[] = "_logger"; +static const char __pyx_k_lstrip[] = "lstrip"; +static const char __pyx_k_module[] = "__module__"; +static const char __pyx_k_name_2[] = "__name__"; +static const char __pyx_k_number[] = "number"; +static const char __pyx_k_object[] = "object"; +static const char __pyx_k_record[] = "record"; +static const char __pyx_k_scan_2[] = "_scan"; +static const char __pyx_k_search[] = "search"; +static const char __pyx_k_string[] = "string_"; +static const char __pyx_k_IOError[] = "IOError"; +static const char __pyx_k_SfError[] = "SfError"; +static const char __pyx_k_authors[] = "__authors__"; +static const char __pyx_k_get_mca[] = "get_mca"; +static const char __pyx_k_getitem[] = "__getitem__"; +static const char __pyx_k_index_2[] = "_index"; +static const char __pyx_k_license[] = "__license__"; +static const char __pyx_k_logging[] = "logging"; +static const char __pyx_k_order_2[] = "_order"; +static const char __pyx_k_os_path[] = "os.path"; +static const char __pyx_k_prepare[] = "__prepare__"; +static const char __pyx_k_version[] = "version"; +static const char __pyx_k_warning[] = "warning"; +static const char __pyx_k_KeyError[] = "KeyError"; +static const char __pyx_k_L_header[] = "L_header"; +static const char __pyx_k_P_Knobel[] = "P. Knobel"; +static const char __pyx_k_Scan_mca[] = "Scan.mca"; +static const char __pyx_k_channels[] = "channels"; +static const char __pyx_k_filename[] = "filename"; +static const char __pyx_k_header_2[] = "header"; +static const char __pyx_k_labels_2[] = "labels"; +static const char __pyx_k_number_2[] = "_number"; +static const char __pyx_k_property[] = "property"; +static const char __pyx_k_qualname[] = "__qualname__"; +static const char __pyx_k_specfile[] = "_specfile"; +static const char __pyx_k_MCA___len[] = "MCA.__len__"; +static const char __pyx_k_Scan_data[] = "Scan.data"; +static const char __pyx_k_TypeError[] = "TypeError"; +static const char __pyx_k_data_line[] = "data_line"; +static const char __pyx_k_enumerate[] = "enumerate"; +static const char __pyx_k_getLogger[] = "getLogger"; +static const char __pyx_k_increment[] = "increment"; +static const char __pyx_k_match_mca[] = "match_mca"; +static const char __pyx_k_mca_index[] = "mca_index"; +static const char __pyx_k_metaclass[] = "__metaclass__"; +static const char __pyx_k_transpose[] = "transpose"; +static const char __pyx_k_11_08_2017[] = "11/08/2017"; +static const char __pyx_k_IndexError[] = "IndexError"; +static const char __pyx_k_MCA___init[] = "MCA.__init__"; +static const char __pyx_k_MCA___iter[] = "MCA.__iter__"; +static const char __pyx_k_Scan_index[] = "Scan.index"; +static const char __pyx_k_Scan_order[] = "Scan.order"; +static const char __pyx_k_Valid_keys[] = "\nValid keys: '"; +static const char __pyx_k_ValueError[] = "ValueError"; +static const char __pyx_k_calib_line[] = "calib_line"; +static const char __pyx_k_chann_line[] = "chann_line"; +static const char __pyx_k_dictionary[] = "dictionary"; +static const char __pyx_k_line_index[] = "line_index"; +static const char __pyx_k_scan_index[] = "scan_index"; +static const char __pyx_k_scan_order[] = "scan_order"; +static const char __pyx_k_specfile_2[] = "specfile"; +static const char __pyx_k_startswith[] = "startswith"; +static const char __pyx_k_ImportError[] = "ImportError"; +static const char __pyx_k_MemoryError[] = "MemoryError"; +static const char __pyx_k_Scan___init[] = "Scan.__init__"; +static const char __pyx_k_Scan_header[] = "Scan.header"; +static const char __pyx_k_Scan_labels[] = "Scan.labels"; +static const char __pyx_k_Scan_number[] = "Scan.number"; +static const char __pyx_k_calib_lines[] = "calib_lines"; +static const char __pyx_k_calibration[] = "calibration"; +static const char __pyx_k_chann_lines[] = "chann_lines"; +static const char __pyx_k_file_header[] = "file_header"; +static const char __pyx_k_is_specfile[] = "is_specfile"; +static const char __pyx_k_motor_names[] = "motor_names"; +static const char __pyx_k_scan_header[] = "scan_header"; +static const char __pyx_k_scan_number[] = "scan_number"; +static const char __pyx_k_RuntimeError[] = "RuntimeError"; +static const char __pyx_k_SfNoMcaError[] = "SfNoMcaError"; +static const char __pyx_k_handle_error[] = "_handle_error"; +static const char __pyx_k_version_info[] = "version_info"; +static const char __pyx_k_MCA___getitem[] = "MCA.__getitem__"; +static const char __pyx_k_SfErrFileOpen[] = "SfErrFileOpen"; +static const char __pyx_k_SfErrFileRead[] = "SfErrFileRead"; +static const char __pyx_k_motor_names_2[] = "_motor_names"; +static const char __pyx_k_number_of_mca[] = "number_of_mca"; +static const char __pyx_k_AttributeError[] = "AttributeError"; +static const char __pyx_k_Scan_data_line[] = "Scan.data_line"; +static const char __pyx_k_SfErrFileClose[] = "SfErrFileClose"; +static const char __pyx_k_SfErrFileWrite[] = "SfErrFileWrite"; +static const char __pyx_k_SfErrLineEmpty[] = "SfErrLineEmpty"; +static const char __pyx_k_parse_channels[] = "_parse_channels"; +static const char __pyx_k_SpecFile___iter[] = "SpecFile.__iter__"; +static const char __pyx_k_mca_header_dict[] = "mca_header_dict"; +static const char __pyx_k_motor_positions[] = "motor_positions"; +static const char __pyx_k_SF_ERR_FILE_OPEN[] = "SF_ERR_FILE_OPEN"; +static const char __pyx_k_SF_ERR_NO_ERRORS[] = "SF_ERR_NO_ERRORS"; +static const char __pyx_k_Scan_file_header[] = "Scan.file_header"; +static const char __pyx_k_Scan_motor_names[] = "Scan.motor_names"; +static const char __pyx_k_Scan_scan_header[] = "Scan.scan_header"; +static const char __pyx_k_SfErrColNotFound[] = "SfErrColNotFound"; +static const char __pyx_k_SfErrMcaNotFound[] = "SfErrMcaNotFound"; +static const char __pyx_k_SfErrMemoryAlloc[] = "SfErrMemoryAlloc"; +static const char __pyx_k_all_calib_values[] = "all_calib_values"; +static const char __pyx_k_all_chann_values[] = "all_chann_values"; +static const char __pyx_k_file_header_dict[] = "_file_header_dict"; +static const char __pyx_k_get_error_string[] = "_get_error_string"; +static const char __pyx_k_scan_header_dict[] = "_scan_header_dict"; +static const char __pyx_k_silx_io_specfile[] = "silx.io.specfile"; +static const char __pyx_k_SfErrLineNotFound[] = "SfErrLineNotFound"; +static const char __pyx_k_SfErrScanNotFound[] = "SfErrScanNotFound"; +static const char __pyx_k_SfErrUserNotFound[] = "SfErrUserNotFound"; +static const char __pyx_k_file_header_lines[] = "_file_header_lines"; +static const char __pyx_k_mca_header_dict_2[] = "_mca_header_dict"; +static const char __pyx_k_motor_positions_2[] = "_motor_positions"; +static const char __pyx_k_parse_calibration[] = "_parse_calibration"; +static const char __pyx_k_scan_header_lines[] = "_scan_header_lines"; +static const char __pyx_k_SfErrLabelNotFound[] = "SfErrLabelNotFound"; +static const char __pyx_k_SfErrMotorNotFound[] = "SfErrMotorNotFound"; +static const char __pyx_k_SfNoMca_returned_1[] = "(SfNoMca returned -1)"; +static const char __pyx_k_add_or_concatenate[] = "_add_or_concatenate"; +static const char __pyx_k_file_header_dict_2[] = "file_header_dict"; +static const char __pyx_k_scan_header_dict_2[] = "scan_header_dict"; +static const char __pyx_k_MCA__parse_channels[] = "MCA._parse_channels"; +static const char __pyx_k_SfErrHeaderNotFound[] = "SfErrHeaderNotFound"; +static const char __pyx_k_data_column_by_name[] = "data_column_by_name"; +static const char __pyx_k_string_to_char_star[] = "_string_to_char_star"; +static const char __pyx_k_Scan_mca_header_dict[] = "Scan.mca_header_dict"; +static const char __pyx_k_Scan_motor_positions[] = "Scan.motor_positions"; +static const char __pyx_k_record_exists_in_hdr[] = "record_exists_in_hdr"; +static const char __pyx_k_SF_ERR_SCAN_NOT_FOUND[] = "SF_ERR_SCAN_NOT_FOUND"; +static const char __pyx_k_Scan_file_header_dict[] = "Scan.file_header_dict"; +static const char __pyx_k_Scan_scan_header_dict[] = "Scan.scan_header_dict"; +static const char __pyx_k_SfErrPositionNotFound[] = "SfErrPositionNotFound"; +static const char __pyx_k_one_line_calib_values[] = "one_line_calib_values"; +static const char __pyx_k_one_line_chann_values[] = "one_line_chann_values"; +static const char __pyx_k_MCA__parse_calibration[] = "MCA._parse_calibration"; +static const char __pyx_k_motor_position_by_name[] = "motor_position_by_name"; +static const char __pyx_k_Scan_data_column_by_name[] = "Scan.data_column_by_name"; +static const char __pyx_k_Scan_record_exists_in_hdr[] = "Scan.record_exists_in_hdr"; +static const char __pyx_k_Scan_motor_position_by_name[] = "Scan.motor_position_by_name"; +static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static const char __pyx_k_Error_while_closing_SpecFile[] = "Error while closing SpecFile"; +static const char __pyx_k_number_and_M_the_order_eg_2_3[] = " number and M the order (eg '2.3')."; +static const char __pyx_k_MCA_index_must_be_in_range_0_d[] = "MCA index must be in range 0-%d"; +static const char __pyx_k_param_specfile_Parent_SpecFile[] = "\n\n :param specfile: Parent SpecFile from which this scan is extracted.\n :type specfile: :class:`SpecFile`\n :param scan_index: Unique index defining the scan in the SpecFile\n :type scan_index: int\n\n Interface to access a SpecFile scan\n\n A scan is a block of descriptive header lines followed by a 2D data array.\n\n Following three ways of accessing a scan are equivalent::\n\n sf = SpecFile(\"/path/to/specfile.dat\")\n\n # Explicit class instantiation\n scan2 = Scan(sf, scan_index=2)\n\n # 0-based index on a SpecFile object\n scan2 = sf[2]\n\n # Using a \"n.m\" key (scan number starting with 1, scan order)\n scan2 = sf[\"3.1\"]\n "; +static const char __pyx_k_Base_exception_inherited_by_all[] = "Base exception inherited by all exceptions raised when a\n C function from the legacy SpecFile library returns an error\n code.\n "; +static const char __pyx_k_Scan_index_must_be_in_range_0_d[] = "Scan index must be in range 0-%d"; +static const char __pyx_k_The_scan_identification_key_can[] = "The scan identification key can be an integer representing "; +static const char __pyx_k_This_module_is_a_cython_binding[] = "\nThis module is a cython binding to wrap the C SpecFile library, to access\nSpecFile data within a python program.\n\nDocumentation for the original C library SpecFile can be found on the ESRF\nwebsite:\n`The manual for the SpecFile Library <http://www.esrf.eu/files/live/sites/www/files/Instrumentation/software/beamline-control/BLISS/documentation/SpecFileManual.pdf>`_\n\nExamples\n========\n\nStart by importing :class:`SpecFile` and instantiate it:\n\n.. code-block:: python\n\n from silx.io.specfile import SpecFile\n\n sf = SpecFile(\"test.dat\")\n\nA :class:`SpecFile` instance can be accessed like a dictionary to obtain a\n:class:`Scan` instance.\n\nIf the key is a string representing two values\nseparated by a dot (e.g. ``\"1.2\"``), they will be treated as the scan number\n(``#S`` header line) and the scan order::\n\n # get second occurrence of scan \"#S 1\"\n myscan = sf[\"1.2\"]\n\n # access scan data as a numpy array\n nlines, ncolumns = myscan.data.shape\n\nIf the key is an integer, it will be treated as a 0-based index::\n\n first_scan = sf[0]\n second_scan = sf[1]\n\nIt is also possible to browse through all scans using :class:`SpecFile` as\nan iterator::\n\n for scan in sf:\n print(scan.scan_header_dict['S'])\n\nMCA spectra can be selectively loaded using an instance of :class:`MCA`\nprovided by :class:`Scan`::\n\n # Only one MCA spectrum is loaded in memory\n second_mca = first_scan.mca[1]\n\n # Iterating trough all MCA spectra in a scan:\n for mca_data in first_scan.mca:\n print(sum(mca_data))\n\nClasses\n=======\n\n- :class:`SpecFile`\n- :class:`Scan`\n- :class:`MCA`\n\nExceptions\n==========\n\n- :class:`SfError`\n- :class:`SfErrMemoryAlloc`\n- :class:`SfErrFileOpen`\n- :class:`SfErrFileClose`\n- :class:`SfErrFileRead`\n- :class:`SfErrFileWrite`\n- :class:`SfErrLineNotFound`\n- :class:`SfErrScanNotFound`\n- :class:`SfErrHeaderNotFound`\n- :class:`SfErrLabelNotFound`\n- :class:`SfErrMotorNotFound`""\n- :class:`SfErrPositionNotFound`\n- :class:`SfErrLineEmpty`\n- :class:`SfErrUserNotFound`\n- :class:`SfErrColNotFound`\n- :class:`SfErrMcaNotFound`\n\n"; +static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; +static const char __pyx_k_param_scan_Parent_Scan_instance[] = "\n\n :param scan: Parent Scan instance\n :type scan: :class:`Scan`\n\n :var calibration: MCA calibration :math:`(a, b, c)` (as in\n :math:`a + b x + c x\302\262`) from ``#@CALIB`` scan header.\n :type calibration: list of 3 floats, default ``[0., 1., 0.]``\n :var channels: MCA channels list from ``#@CHANN`` scan header.\n In the absence of a ``#@CHANN`` header, this attribute is a list\n ``[0, \342\200\246, N-1]`` where ``N`` is the length of the first spectrum.\n In the absence of MCA spectra, this attribute defaults to ``None``.\n :type channels: list of int\n\n This class provides access to Multi-Channel Analysis data. A :class:`MCA`\n instance can be indexed to access 1D numpy arrays representing single\n MCA\302\240spectra.\n\n To create a :class:`MCA` instance, you must provide a parent :class:`Scan`\n instance, which in turn will provide a reference to the original\n :class:`SpecFile` instance::\n\n sf = SpecFile(\"/path/to/specfile.dat\")\n scan2 = Scan(sf, scan_index=2)\n mcas_in_scan2 = MCA(scan2)\n for i in len(mcas_in_scan2):\n mca_data = mcas_in_scan2[i]\n ... # do some something with mca_data (1D numpy array)\n\n A more pythonic way to do the same work, without having to explicitly\n instantiate ``scan`` and ``mcas_in_scan``, would be::\n\n sf = SpecFile(\"specfilename.dat\")\n # scan2 from previous example can be referred to as sf[2]\n # mcas_in_scan2 from previous example can be referred to as scan2.mca\n for mca_data in sf[2].mca:\n ... # do some something with mca_data (1D numpy array)\n\n "; +static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; +static const char __pyx_k_users_kieffer_workspace_400_rel[] = "/users/kieffer/workspace-400/release/silx/silx/io/specfile.pyx"; +static const char __pyx_k_Cannot_get_data_column_s_in_scan[] = "Cannot get data column %s in scan %d.%d"; +static const char __pyx_k_Custom_exception_raised_when_SfN[] = "Custom exception raised when ``SfNoMca()`` returns ``-1``\n "; +static const char __pyx_k_Failed_to_retrieve_number_of_MCA[] = "Failed to retrieve number of MCA "; +static const char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; +static const char __pyx_k_MCA_calibration_line_CALIB_not_f[] = "MCA calibration line (@CALIB) not found"; +static const char __pyx_k_MCA_index_should_be_an_integer_s[] = "MCA index should be an integer (%s provided)"; +static const char __pyx_k_No_MCA_spectrum_found_in_this_sc[] = "No MCA spectrum found in this scan"; +static const char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static const char __pyx_k_Parameter_value_must_be_a_string[] = "Parameter value must be a string."; +static const char __pyx_k_Unable_to_parse_file_header_line[] = "Unable to parse file header line "; +static const char __pyx_k_Unable_to_parse_scan_header_line[] = "Unable to parse scan header line "; +static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; +static const char __pyx_k_the_unique_scan_index_or_a_strin[] = "the unique scan index or a string 'N.M' with N being the scan"; +static const char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; static PyObject *__pyx_kp_s_; +static PyObject *__pyx_kp_s_11_08_2017; static PyObject *__pyx_kp_s_2; -static PyObject *__pyx_kp_s_27_09_2016; static PyObject *__pyx_kp_s_3; static PyObject *__pyx_n_s_AttributeError; static PyObject *__pyx_kp_s_Base_exception_inherited_by_all; @@ -1658,11 +1987,12 @@ static PyObject *__pyx_kp_s_Cannot_get_data_column_s_in_scan; static PyObject *__pyx_kp_s_Custom_exception_raised_when_SfN; static PyObject *__pyx_n_s_ERRORS; static PyObject *__pyx_kp_s_Error_while_closing_SpecFile; -static PyObject *__pyx_n_s_Exception; static PyObject *__pyx_kp_s_F; static PyObject *__pyx_kp_s_Failed_to_retrieve_number_of_MCA; static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; +static PyObject *__pyx_n_s_IOError; +static PyObject *__pyx_n_s_ImportError; static PyObject *__pyx_n_s_IndexError; static PyObject *__pyx_n_s_KeyError; static PyObject *__pyx_n_s_L; @@ -1678,6 +2008,7 @@ static PyObject *__pyx_kp_s_MCA_calibration_line_CALIB_not_f; static PyObject *__pyx_kp_s_MCA_index_must_be_in_range_0_d; static PyObject *__pyx_kp_s_MCA_index_should_be_an_integer_s; static PyObject *__pyx_n_s_MIT; +static PyObject *__pyx_n_s_MemoryError; static PyObject *__pyx_kp_s_No_MCA_spectrum_found_in_this_sc; static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; static PyObject *__pyx_kp_s_P_Knobel; @@ -1745,7 +2076,6 @@ static PyObject *__pyx_n_s_append; static PyObject *__pyx_n_s_args; static PyObject *__pyx_n_s_ascii; static PyObject *__pyx_n_s_authors; -static PyObject *__pyx_n_s_basicConfig; static PyObject *__pyx_n_s_calib_line; static PyObject *__pyx_n_s_calib_lines; static PyObject *__pyx_n_s_calibration; @@ -1833,6 +2163,8 @@ static PyObject *__pyx_n_s_number_2; static PyObject *__pyx_kp_s_number_and_M_the_order_eg_2_3; static PyObject *__pyx_n_s_number_of_mca; static PyObject *__pyx_n_s_numpy; +static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to; +static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor; static PyObject *__pyx_n_s_object; static PyObject *__pyx_n_s_one_line_calib_values; static PyObject *__pyx_n_s_one_line_chann_values; @@ -1867,6 +2199,7 @@ static PyObject *__pyx_n_s_search; static PyObject *__pyx_n_s_self; static PyObject *__pyx_n_s_send; static PyObject *__pyx_n_s_shape; +static PyObject *__pyx_n_s_silx_io_specfile; static PyObject *__pyx_n_s_specfile; static PyObject *__pyx_n_s_specfile_2; static PyObject *__pyx_n_s_split; @@ -1883,13 +2216,75 @@ static PyObject *__pyx_kp_s_the_unique_scan_index_or_a_strin; static PyObject *__pyx_n_s_throw; static PyObject *__pyx_n_s_transpose; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; -static PyObject *__pyx_kp_s_users_payno_Documents_dev_esrf; +static PyObject *__pyx_kp_s_users_kieffer_workspace_400_rel; static PyObject *__pyx_n_s_value; static PyObject *__pyx_n_s_version; static PyObject *__pyx_n_s_version_info; static PyObject *__pyx_kp_s_w; static PyObject *__pyx_kp_s_w_2; static PyObject *__pyx_n_s_warning; +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_scan); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_2_parse_channels(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_4_parse_calibration(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_6__len__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_8__getitem__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_10__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile__add_or_concatenate(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_dictionary, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_specfile, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_2index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_4number(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_6order(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_8header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_10scan_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_12file_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_14scan_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_16mca_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_18file_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_20labels(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_22data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_24mca(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_26motor_names(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_28motor_positions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_30record_exists_in_hdr(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_record); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_32data_line(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_34data_column_by_name(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_label); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_36motor_position_by_name(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_2_string_to_char_star(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string_); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4is_specfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename); /* proto */ +static int __pyx_pf_4silx_2io_8specfile_8SpecFile___cinit__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ +static int __pyx_pf_4silx_2io_8specfile_8SpecFile_2__init__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ +static void __pyx_pf_4silx_2io_8specfile_8SpecFile_4__dealloc__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_pf_4silx_2io_8specfile_8SpecFile_6__len__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_8__iter__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_11__getitem__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_13keys(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static int __pyx_pf_4silx_2io_8specfile_8SpecFile_15__contains__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_17_get_error_string(CYTHON_UNUSED struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_error_code); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_19_handle_error(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_error_code); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_21index(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_number, PyObject *__pyx_v_scan_order); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_23number(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_25order(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_27_list(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_29list(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_31data(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_33data_column_by_name(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_label); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_35scan_header(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_37file_header(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_39columns(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_41command(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_43date(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_45labels(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_47motor_names(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_49motor_positions(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_51motor_position_by_name(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_53number_of_mca(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_55mca_calibration(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_57get_mca(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_mca_index); /* proto */ +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ +static PyObject *__pyx_tp_new_4silx_2io_8specfile_SpecFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_4silx_2io_8specfile___pyx_scope_struct____iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_4silx_2io_8specfile___pyx_scope_struct_1___iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_float_0_; static PyObject *__pyx_float_1_; static PyObject *__pyx_int_0; @@ -1931,6 +2326,7 @@ static PyObject *__pyx_tuple__22; static PyObject *__pyx_tuple__23; static PyObject *__pyx_tuple__24; static PyObject *__pyx_tuple__26; +static PyObject *__pyx_tuple__29; static PyObject *__pyx_tuple__30; static PyObject *__pyx_tuple__31; static PyObject *__pyx_tuple__32; @@ -1939,6 +2335,7 @@ static PyObject *__pyx_tuple__34; static PyObject *__pyx_tuple__35; static PyObject *__pyx_tuple__36; static PyObject *__pyx_tuple__37; +static PyObject *__pyx_tuple__38; static PyObject *__pyx_tuple__39; static PyObject *__pyx_tuple__41; static PyObject *__pyx_tuple__43; @@ -1966,7 +2363,7 @@ static PyObject *__pyx_tuple__85; static PyObject *__pyx_tuple__87; static PyObject *__pyx_tuple__89; static PyObject *__pyx_tuple__91; -static PyObject *__pyx_codeobj__38; +static PyObject *__pyx_tuple__93; static PyObject *__pyx_codeobj__40; static PyObject *__pyx_codeobj__42; static PyObject *__pyx_codeobj__44; @@ -1994,8 +2391,9 @@ static PyObject *__pyx_codeobj__86; static PyObject *__pyx_codeobj__88; static PyObject *__pyx_codeobj__90; static PyObject *__pyx_codeobj__92; +static PyObject *__pyx_codeobj__94; -/* "specfile.pyx":234 +/* "silx/io/specfile.pyx":233 * * """ * def __init__(self, scan): # <<<<<<<<<<<<<< @@ -2004,15 +2402,12 @@ static PyObject *__pyx_codeobj__92; */ /* Python wrapper */ -static PyObject *__pyx_pw_8specfile_3MCA_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_8specfile_3MCA___init__[] = "MCA.__init__(self, scan)"; -static PyMethodDef __pyx_mdef_8specfile_3MCA_1__init__ = {"__init__", (PyCFunction)__pyx_pw_8specfile_3MCA_1__init__, METH_VARARGS|METH_KEYWORDS, __pyx_doc_8specfile_3MCA___init__}; -static PyObject *__pyx_pw_8specfile_3MCA_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_4silx_2io_8specfile_3MCA_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_4silx_2io_8specfile_3MCA___init__[] = "MCA.__init__(self, scan)"; +static PyMethodDef __pyx_mdef_4silx_2io_8specfile_3MCA_1__init__ = {"__init__", (PyCFunction)__pyx_pw_4silx_2io_8specfile_3MCA_1__init__, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_3MCA___init__}; +static PyObject *__pyx_pw_4silx_2io_8specfile_3MCA_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_scan = 0; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); @@ -2036,11 +2431,11 @@ static PyObject *__pyx_pw_8specfile_3MCA_1__init__(PyObject *__pyx_self, PyObjec case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_scan)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, 1); __PYX_ERR(0, 233, __pyx_L3_error) } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) __PYX_ERR(0, 233, __pyx_L3_error) } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; @@ -2053,74 +2448,71 @@ static PyObject *__pyx_pw_8specfile_3MCA_1__init__(PyObject *__pyx_self, PyObjec } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 233, __pyx_L3_error) __pyx_L3_error:; - __Pyx_AddTraceback("specfile.MCA.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("silx.io.specfile.MCA.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_8specfile_3MCA___init__(__pyx_self, __pyx_v_self, __pyx_v_scan); + __pyx_r = __pyx_pf_4silx_2io_8specfile_3MCA___init__(__pyx_self, __pyx_v_self, __pyx_v_scan); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_8specfile_3MCA___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_scan) { +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_scan) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__init__", 0); - /* "specfile.pyx":235 + /* "silx/io/specfile.pyx":234 * """ * def __init__(self, scan): * self._scan = scan # <<<<<<<<<<<<<< * * # Header dict */ - if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_scan_2, __pyx_v_scan) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_scan_2, __pyx_v_scan) < 0) __PYX_ERR(0, 234, __pyx_L1_error) - /* "specfile.pyx":238 + /* "silx/io/specfile.pyx":237 * * # Header dict * self._header = scan.mca_header_dict # <<<<<<<<<<<<<< * * self.calibration = [] */ - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_scan, __pyx_n_s_mca_header_dict); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 238; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_scan, __pyx_n_s_mca_header_dict); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 237, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_header, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 238; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_header, __pyx_t_1) < 0) __PYX_ERR(0, 237, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "specfile.pyx":240 + /* "silx/io/specfile.pyx":239 * self._header = scan.mca_header_dict * * self.calibration = [] # <<<<<<<<<<<<<< * """List of lists of calibration values, * one list of 3 floats per MCA device or a single list applying to */ - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 239, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_calibration, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_PyObject_SetAttrStr(__pyx_v_self, __pyx_n_s_calibration, __pyx_t_1) < 0) __PYX_ERR(0, 239, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "specfile.pyx":244 + /* "silx/io/specfile.pyx":243 * one list of 3 floats per MCA device or a single list applying to * all devices """ * self._parse_calibration() # <<<<<<<<<<<<<< * * self.channels = [] */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse_calibration); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self, __pyx_n_s_parse_calibration); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 243, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); 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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L0; + + /* "silx/io/specfile.pyx":559 + * """ + * for line in self._header: + * if line.startswith("#" + record): # <<<<<<<<<<<<<< + * return True + * return False + */ } - /* "specfile.pyx":560 + /* "silx/io/specfile.pyx":558 * :rtype: boolean * """ * for line in self._header: # <<<<<<<<<<<<<< @@ -6520,7 +7466,7 @@ static PyObject *__pyx_pf_8specfile_4Scan_30record_exists_in_hdr(CYTHON_UNUSED P } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "specfile.pyx":563 + /* "silx/io/specfile.pyx":561 * if line.startswith("#" + record): * return True * return False # <<<<<<<<<<<<<< @@ -6532,7 +7478,7 @@ static PyObject *__pyx_pf_8specfile_4Scan_30record_exists_in_hdr(CYTHON_UNUSED P __pyx_r = Py_False; goto __pyx_L0; - /* "specfile.pyx":546 + /* "silx/io/specfile.pyx":544 * return self._motor_positions * * def record_exists_in_hdr(self, record): # <<<<<<<<<<<<<< @@ -6548,7 +7494,7 @@ static PyObject *__pyx_pf_8specfile_4Scan_30record_exists_in_hdr(CYTHON_UNUSED P __Pyx_XDECREF(__pyx_t_6); 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- goto __pyx_L3; + + /* "silx/io/specfile.pyx":685 + * """Destructor: Calls SfClose(self.handle)""" + * # handle is NULL if SfOpen failed + * if self.handle: # <<<<<<<<<<<<<< + * if specfile_wrapper.SfClose(self.handle): + * _logger.warning("Error while closing SpecFile") + */ } - __pyx_L3:; - /* "specfile.pyx":686 + /* "silx/io/specfile.pyx":682 * self.filename = filename * * def __dealloc__(self): # <<<<<<<<<<<<<< * """Destructor: Calls SfClose(self.handle)""" - * #SfClose makes a segmentation fault if file failed to open + * # handle is NULL if SfOpen failed */ /* function exit code */ @@ -8310,12 +9478,12 @@ static void __pyx_pf_8specfile_8SpecFile_4__dealloc__(struct __pyx_obj_8specfile __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); - __Pyx_WriteUnraisable("specfile.SpecFile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 0); + __Pyx_WriteUnraisable("silx.io.specfile.SpecFile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename, 0, 0); __pyx_L0:; 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